3&#39;-oh unblocked, fast photocleavable terminating nucleotides and methods for nucleic acid sequencing

ABSTRACT

The present invention relates generally to 3′-OH unblocked nucleotides and nucleosides labeled and unlabeled with 5-methoxy-substituted nitrobenzyl-based photocleavable terminating groups for use in methods and systems related to DNA and RNA sequencing and analysis. These compounds may be used as reversible terminators as they exhibit fast nucleotide incorporation kinetics, single-base termination, high nucleotide selectivity, and rapid terminating group cleavage that results in a naturally occurring nucleotide.

The present application is a divisional patent application of co-pendingU.S. patent application Ser. No. 13/615,284, filed Sep. 13, 2012, whichclaims the benefit of priority to U.S. Provisional Application No.61/627,211, filed Oct. 7, 2011, and U.S. Provisional Application No.61/534,347, filed Sep. 13, 2011. The contents of each of theabove-referenced applications are incorporated herein by reference.

BACKGROUND OF THE INVENTION

I. Field of the Invention

The present invention relates generally to compositions and methods forDNA sequencing and other types of DNA analysis. More particularly, theinvention relates in part to fast 3′-OH unblocked nucleotides andnucleosides with photochemically cleavable groups and methods for theiruse in a number of DNA sequencing methods, including applications inbiomedical research.

II. Description of Related Art

Methods for rapidly sequencing DNA are needed for analyzing diseases andmutations in the population and developing therapies (Metzker, 2010,which is incorporated herein by reference). Commonly observed forms ofhuman sequence variation are single nucleotide polymorphisms (SNPs),which occur in approximately 1-in-300 to 1-in-1000 base pairs of genomicsequence and structural variants (SVs) including block substitutions,insertion/deletions, inversions, segmental duplications, and copy numbervariants. Structural variants can account for 22% of all variable eventsand more variant bases than those contributed by SNPs (Levy et al.,2007, which is incorporated herein by reference). This finding isconsistent with that of Scherer, Hurles, and colleagues who analyzed 270individuals using microarray based methods (Redon et al., 2006, which isincorporated herein by reference). Building upon the complete sequenceof the human genome, efforts are underway to identify the underlyinggenetic link to common diseases and cancer by SNP and SV mapping ordirect association. Technology developments focused on rapid,high-throughput, and low cost DNA sequencing would facilitate theunderstanding and use of genetic information, such as SNPs and SVs, inapplied medicine.

In general, 10%-to-15% of SNPs will affect protein function by alteringspecific amino acid residues, will affect the proper processing of genesby changing splicing mechanisms, or will affect the normal level ofexpression of the gene or protein by varying regulatory mechanisms. SVsmay also play an important role in human biology and disease (Iafrate etal., 2004; Sebat et al., 2004; Tuzun et al., 2005; Stranger et al.,2007, which are incorporated herein by reference). It is envisioned thatthe identification of informative SNPs and SVs will lead to moreaccurate diagnosis of inherited disease, better prognosis of risksusceptibilities, or identity of sporadic mutations in tissue. Oneapplication of an individual's SNP and SV profile would be tosignificantly delay the onset or progression of disease withprophylactic drug therapies. Moreover, an SNP and SV profile of drugmetabolizing genes could be used to prescribe a specific drug regimen toprovide safer and more efficacious results. To accomplish theseambitious goals, genome sequencing will move into the resequencing phasewith the potential of partial sequencing of a large majority of thepopulation, which would involve sequencing specific regions in parallel,which are distributed throughout the human genome to obtain the SNP andSV profile for a given complex disease.

Sequence variations underlying most common diseases are likely toinvolve multiple SNPs, SVs, and a number of combinations thereof, whichare dispersed throughout associated genes and exist in low frequency.Thus, DNA sequencing technologies that employ strategies for de novosequencing are more likely to detect and/or discover these rare, widelydispersed variants than technologies targeting only known SNPs.

One example how NGS technologies can be applied in the detection ofSNPs, SVs, single nucleotide variants (SNVs) and a number ofcombinations thereof is cancer diagnostics. These assays havetraditionally been a single-marker, single-assay approach that hasrecently progressed to assaying multiple markers with a singleexperimental approach. However, each cancer is genetically complex oftenwith many mutations occurring simultaneously in numerous genes.Therefore, traditional methods lead to expensive and time-consumingtesting, while providing information only on a select few of knownsequence variants. Recent advances in NGS technologies have allowedtargeted approaches that center on many medically actionable genetargets associated with various cancer types (See Su et al., 2011;Beadling et al. 2012). Due to recent successes of sequencing efforts,such as The Cancer Genome Atlas (TCGA) project, the International CancerGenome Consortium (ICGC) project, and the Catalogue of Somatic Mutationsin Cancer (COSMIC) database, there is a large compendium of knowledgeregarding these gene targets in many cancer types and the result oftherapeutics on cancers containing those mutations (See Futreal et al.,2004). Additional work, in part as a result of the Pediatric CancerGenome Project, has shown that pediatric cancers have distinct geneticprofiles marked by a fewer number of mutations and a prevalence ofmutations in alternative molecular pathways (See, Wu et al., 2012;Meldrum et al. 2011). The largest current unmet need in cancerdiagnostics is a fast, high-throughput technology with the neededaccuracy and sensitivity for early-stage detection to identify raresequence variants that belong to a limited subpopulation of cellsundergoing a cancerous transformation.

Traditionally, DNA sequencing has been accomplished by the “Sanger” or“dideoxy” method, which involves the chain termination of DNA synthesisby the incorporation of 2′,3′-dideoxynucleotides (ddNTPs) using DNApolymerase (Metzker et al., 2005, which is incorporated herein byreference). Since 2005, there has been a fundamental shift away from theapplication of automated Sanger sequencing for genome analysis.Advantages of next-generation sequencing (NGS) technologies include theability to produce an enormous volume of data cheaply, in some cases inexcess of a hundred million short sequence reads per instrument run.Many of these approaches are commonly referred to assequencing-by-synthesis (SBS), which does not clearly delineate thedifferent mechanics of sequencing DNA (Metzker, 2010; Metzker 2005,which are incorporated herein by reference). DNA polymerase-dependentstrategies have been classified as cyclic reversible termination (CRT),single nucleotide addition (SNA, e.g., pyrosequencing), and real-timesequencing. An approach whereby DNA polymerase is replaced by DNA ligaseis referred to as sequencing-by-ligation (SBL). These approaches havebeen described in Metzker (2010), which is incorporated herein byreference.

Sequencing technologies include a number of methods that are groupedbroadly as (a) template preparation, (b) sequencing and imaging, and (c)data analysis. The unique combination of specific protocolsdistinguishes one technology from another and determines the type ofdata produced from each platform. These differences in data outputpresent challenges when comparing platforms based on data quality andcost. Although quality scores and accuracy estimates are provided byeach manufacturer, there is no consensus that a ‘quality base’ from oneplatform is equivalent to that from another platform.

Two methods used in preparing templates for NGS reactions include:clonally amplified templates originating from single DNA molecules andsingle DNA molecule templates. Sequencing methods that use DNApolymerases are classified as cyclic reversible termination (CRT),single-nucleotide addition (SNA) and real-time sequencing, (See Metzker2010). Sequencing by ligation (SBL), an approach in which DNA polymeraseis replaced by DNA ligase, has also been used in the NGS technologies,(see, e.g., Shendure et al., 2005; Valouev et al., 2008). Imagingmethods coupled with these sequencing strategies range from measuringbioluminescent signals to four-color imaging of single molecular events.The voluminous data produced by these NGS platforms place substantialdemands on information technology in terms of data storage, tracking andquality control (see Pop & Salzberg, 2008).

The need for robust methods that produce a representative, non-biasedsource of nucleic acid material from the genome under investigationremains an important goal. Current methods generally involve randomlybreaking genomic DNA into smaller sizes from which either fragmenttemplates or mate-pair templates are created. A common theme among NGStechnologies is that the template is attached or immobilized to a solidsurface or support. The immobilization of spatially separated templatesites allows thousands to billions of sequencing reactions to beperformed simultaneously.

Although clonally amplified methods offer certain advantages overbacterial cloning, some of the protocols are typically cumbersome toimplement and require a large amount of genomic DNA material (3-20 μg).The preparation of single-molecule templates is more straightforward andrequires less starting material (<1 μg). Moreover, these methods do notrequire PCR, which creates mutations in clonally amplified templatesthat masquerade as sequence variants. AT-rich and GC-rich targetsequences may also show amplification bias in product yield, whichresults in their underrepresentation in genome alignments andassemblies. Quantitative applications, such as RNA-seq (See Wang et al.,2009), perform more effectively with non-amplified template sources,which do not alter the representational abundance of mRNA molecules.

An important aspect of the CRT method is the reversible terminator, ofwhich there are two main types: 3′-O-blocked and 3′-OH unblocked(Metzker, 2010). The use of a ddNTP, which acts as a chain terminator inSanger sequencing, provided the basis for the initial development ofreversible blocking groups attached to the 3′-end of nucleotides(Metzker et al. 1994; Canard & Sarfati, 1994). Blocking groups such as3′-O-allyl-dNTPs (Metzker et al., 1994; U.S. Pat. No. 6,664,079; Ju etal., 2006; U.S. Pat. No. 7,057,026; U.S. Pat. No. 7,345,159; U.S. Pat.No. 7,635,578; U.S. Pat. No. 7,713,698) and 3′-O-azidomethyl-dNTPs (U.S.Pat. No. 7,057,026; Guo et al., 2008; Bentley et al., 2008; U.S. Pat.No. 7,414,116; U.S. Pat. No. 7,541,444; U.S. Pat. No. 7,592,435; U.S.Pat. No. 7,556,537; U.S. Pat. No. 7,771,973) have been used in CRT.3′-O-Blocked terminators require the cleavage of two chemical bonds toremove the fluorophore from the nucleobase and restore the 3′-OH group.A drawback in using these reversible terminators is that the blockinggroup attached to the 3′-end typically causes a bias againstincorporation with DNA polymerase. Mutagenesis of DNA polymerase isoften required to facilitate incorporation of 3′-O-blocked terminators.Large numbers of genetically engineered DNA polymerases have to becreated by either site-directed or random mutagenesis containing one ormore amino acid substitutions, insertions, and/or deletions and thenidentified by high-throughput screening with the goal of incorporating3′-blocked nucleotides more efficiently.

The difficulty in identifying a modified enzyme that efficientlyincorporates 3′-O-blocked terminators by screening large libraries ofmutant DNA polymerases has led to the development of 3′-unblockedreversible terminators. It was demonstrated that a small photocleavablegroup attached to the base of a 3′-OH unblocked nucleotide can act as aneffective reversible terminator and be efficiently incorporated bywild-type DNA polymerases (Wu et al., 2007; Metzker, 2010; Litosh etal., 2011, Gardner et al., 2012; U.S. Pat. Nos. 7,897,737, 7,964,352;and 8,148,503, U.S. Patent Appl. Publication 2011/0287427). For example,5-hydroxymethyl-2′-deoxyuridine (HOMedU) is found naturally in thegenomes of numerous bacteriophages and lower eukaryotes (Gommers-Ampt,1995, which is incorporated herein by reference). Its hydroxymethylgroup can serve as molecular handle to attach a small photocleavableterminating group. Other naturally occurring hypermodified bases thatcan be further modified to function as reversible terminators include5-hydroxymethyl-2′-deoxycytidine (HOMedC), which is found naturally inthe genomes of T2, T4, and T6 bacteriophages (Wyatt & Cohen, 1953;Gommers-Ampt, 1995) and of mammals (Kriaucionis & Heintz, 2009;Tahiliani et al., 2009; Ito et al., 2010). The pyrrolopyrimidine ringstructure (7-deazapurine) is also found naturally in nucleosideantibiotics (Carrasco & Vázquez, 1984, which is incorporated herein byreference) and tRNA bases (Limbach, et al., 1994, which is incorporatedherein by reference), and the compounds7-deaza-7-hydroxymethyl-2′-deoxyadenosine (C⁷-HOMedA) (Rockhill et al.,1997) and 7-deaza-7-hydroxymethyl-2′-deoxyguanosine (C⁷-HOMedG)(McDougall et al., 2001) have been reported.

One aspect of the present invention is the use of a modified2-nitrobenzyl group attached to the nucleobase of hydroxymethylnucleoside and nucleotides. Described over a half century ago, solutionsof 2-nitrotoluene (Wettermark, 1962) and its derivatives (Wettermark,1962; Hardwick et al., 1960; Mosher et al., 1960; Sousa & Weinstein,1962; Weinstein et al., 1966) were reported to exhibit the property ofphotochromism, a phenomenon considered to be the result of transientformation of an aci-nitro anion intermediate (Weinstein et al., 1966;Morrison, 1969). Without being bound by theory, it is generally acceptedthat absorption of a photon by the nitro group results in hydrogenabstraction from the α-carbon (Mosher et al., 1960; Berson & Brown,1955; De Mayo, 1960), formation of the aci-nitro anion intermediate, andthen release of the ‘caged’ effector molecule and creation of anitrosocarbonyl by-product (Corrie, 2005). These early studies suggestedthat α-substitution of the benzylic carbon (Wettermark, 1962) orsubstitution of the 4-position of the benzene ring with anelectron-donating group (Sousa & Weinstein, 1962; Weinstein et al, 1966)increased the rate of the photochromic effect. These findings led to thedevelopment of photosensitive 2-nitrobenzyl protecting groups (Barltropet al., 1966; Patchornik, 1968; Patchornik et al., 1970). The degree towhich the rate of photochemical cleavage is altered, however, typicallydepends on numerous factors that are reported to include substitution ofthe benzylic carbon (Walker et al., 1986; Hasan et al., 1997; Giegrichet al., 1998), functional group(s) attached to the benzyl ring (Wootton& Trentham, 1989; Hasan et al., 1997; Giegrich et al., 1998), and theleaving group (Walker et al., 1986) as well as pH (McCray et al., 1980;Walker et al., 1986; Wootton & Trentham, 1989), solvent (Sousa &Weinstein, 1962; McGall et al., 1997; Giegrich et al., 1998), and lightintensity (McCray et al., 1980; McGall et al., 1997). One property,however, that has not been studied is stereochemistry, whereby,substitution of 2-nitrobenzyl's benzylic or α-carbon results in a chiralcenter. For the case of nucleotide synthesis, coupling of a racemicα-substituted 2-nitrobenzyl alcohol would result in two diastereomers,which differ only by the absolute configuration (R or S) at the benzyliccarbon.

Another class of 3′-OH unblocked nucleotides has been described by Mitraet al. (2003) and Turcatti et al. (2008), which rely on steric hindranceof the bulky dye group to stop incorporation after the addition of thefirst nucleotide. It is noted that the substituted 2-nitrobenzylnucleotide analogs described by Wu et al. (2007), Litosh et al. (2011),and Gardner et al., 2012 cause termination of DNA synthesis without therequirement of bulky substituents such as fluorescent dyes. A furtherclass of 3′-unblocked nucleotides has been described by HelicosBiosciences. These nucleotides use a second nucleoside or nucleotideanalog that acts as an inhibitor of DNA synthesis (Bowers et al., 2009;U.S. Pat. No. 7,476,734). A significant difference in terminationproperties is observed when comparing compounds of the present inventionwith those described by Bowers. For example, Bowers et al. describedpre-steady-state kinetics employing two-base homopolymer templates, forwhich k_(pol(+2)) rates were measured for all of their 3′-OH unblocked‘virtual’ terminators. Bowers et al. conducted their terminationexperiments at submicromolar nucleotide concentrations (i.e., from 100to 250 nM), termination assays. In contrast, several compounds of thepresent invention were performed at 10 μM over the time course of 0.5 to20 min. Both compounds dU.V and dU.VI were rapidly incorporated at thefirst base position (100% by 2 min) and then terminated DNA synthesis atthat position. No appreciable signal could be detected at the expectedsecond-base position up to incubation times of 20 min. See Gardner etal., 2012 for more details.

3′-OH unblocked reversible terminators typically have several advantagesover 3′-O-blocked nucleotides. For example, for many 3′-OH unblockedreversible terminators the cleavage of only a single bond removes boththe terminating and fluorophore groups from the nucleobase. This in turnresults in a more efficient strategy for restoring the nucleotide forthe next CRT cycle. A second advantage of 3′-OH unblocked reversibleterminators is that many of these compounds show more favorableenzymatic incorporation and, in some cases, can be incorporated as wellas a natural nucleotide with wild-type DNA polymerases (Wu et al., 2007;Litosh et al., 2011; Gardner et al., 2012; U.S. Pat. No. 7,897,737; U.S.Pat. No. 7,964,352; U.S. Pat. No. 8,148,503; U.S. Patent Appl.Publication 2011/0287427), although in other cases this efficiency hasnot been observed (Bowers et al., 2009; U.S. Pat. No. 7,476,734). Onechallenge for 3′-OH unblocked terminators is creating the appropriatemodifications to the base that lead to termination of DNA synthesisafter a single base addition. This is important because an unblocked3′-OH group is the natural substrate for incorporating the next incomingnucleotide.

Next-generation sequencing (NGS) technologies have facilitated importantbiomedical discoveries, yet chemistry improvements are still needed fora number of reasons, including reduction of error rates, reduction ofslow cycle times. To be effective in NGS assays, it is typicallydesirable for reversible terminators to exhibit a number of idealproperties including, for example, fast kinetics of nucleotideincorporation, single-base termination, high nucleotide selectivity,and/or rapid cleavage of the terminating group. Thus, there is a needfor developing new nucleosides and nucleotides that meet thesechallenges.

SUMMARY OF THE INVENTION

In some aspects, the present disclosure provides novel compounds andcompositions that are useful in efficient sequencing of genomicinformation in high throughput sequencing reactions. In another aspect,reagents and combinations of reagents that can efficiently andaffordably provide genomic information are provided. In further aspects,the present invention provides libraries and arrays of reagents fordiagnostic methods and for developing targeted therapeutics forindividuals.

In some aspects, the present disclosure provides new compounds that maybe used in DNA sequencing. For example, the present disclosure providescompounds of the formula:

wherein:

-   -   R₁ is hydroxy, monophosphate, diphosphate, triphosphate,        α-thiotriphosphate or polyphosphate;    -   R₂ is hydrogen or hydroxy;    -   R₃ is alkyl_((C≦8)) or substituted alkyl_((C≦8));    -   R₄ is        -   hydrogen, hydroxy, halo, amino, nitro, cyano, azido or            mercapto;        -   alkyl_((C≦6)), acyl_((C≦6)), alkoxy_((C≦6)),            acyloxy_((C≦6)), alkylamino_((C≦6)), dialkyl-amino_((C≦6)),            amido_((C≦6)), or a substituted version of any of these            groups;    -   R₅ and R₆ are each independently:        -   hydrogen, hydroxy, halo, amino, nitro, cyano, azido or            mercapto;        -   alkyl_((C≦6)), alkenyl_((C≦6)), alkynyl_((C≦6)),            aryl_((C≦6)), aralkyl_((C≦8)), heteroaryl_((C≦6)),            acyl_((C≦6)), alkoxy_((C≦6)), acyloxy_((C≦6)),            alkylamino_((C≦6)), dialkyl-amino_((C≦6)), amido_((C≦6)), or            a substituted version of any of these groups;        -   a group of formula:

-   -   -   -   wherein                -   X is                -    —O—, —S—, or —NH—; or                -    alkanediyl_((C≦12)), alkenediyl_((C≦12)),                    alkynediyl_((C≦12)), or a substituted version of any                    of these groups;                -   Y is —O—, —NH—, alkanediyl_((C≦12)) or substituted                    alkane-diyl_((C≦12));                -   n is an integer from 0-6; and                -   m is an integer from 0-6; or

        -   a -linker-reporter;            or a salt, tautomer, or optical isomer thereof.

In some embodiments, the compounds are further defined as a compound offormulas I, II, III, IV, V, VI or VII. In some embodiments, R₁ ishydroxy, monophosphate, diphosphate, triphosphate, α-thiotriphosphate,or polyphosphate.

In some embodiments, R₂ is hydrogen, hydroxy. In some embodiments, R₃ isalkyl_((C≦8)), for example, alkyl_((C3-4)), including isopropyl ortert-butyl. In some embodiments, R₄ is hydrogen, nitro. In someembodiments, R₅ is hydrogen, iodo, or alkoxy_((C≦6)), including, forexample, methoxy. In some embodiments, R₅ is a group of formula:

wherein

X is

-   -   —O—, —S—, or —NH—; or    -   alkanediyl_((C≦12)), alkenediyl_((C≦12)), alkynediyl_((C≦12)),        arenediyl_((C≦12)), heteroarenediyl_((C≦12)), or a substituted        version of any of these groups; and

n is an integer from 0-6.

In some embodiments, X is alkynediyl_((C2-8)), for example, —C≡C—. Insome embodiments, n is zero. In some embodiments, R₅ is a group offormula:

wherein

X is

-   -   —O—, —S—, or —NH—; or    -   alkanediyl_((C≦12)), alkenediyl_((C≦12)), alkynediyl_((C≦12)),        arenediyl_((C≦12)), heteroarenediyl_((C≦12)), or a substituted        version of any of these groups;

Y is —O—, —NH—, alkanediyl_((C≦12)) or substituted alkanediyl_((C≦12));

n is an integer from 0-6; and

m is an integer from 0-6.

In some embodiments, X is alkynediyl_((C2-8)), for example, —C≡C—. Insome embodiments, Y is —CH₂—. In some embodiments, n is zero. In someembodiments, m is zero. In some embodiments, R₅ is a -linker-reporter.In some embodiments, the linker is:

wherein

X is

-   -   —O—, —S—, or —NH—; or    -   alkanediyl_((C≦12)), alkenediyl_((C≦12)), alkynediyl_((C≦12)),        arenediyl_((C≦12)), heteroarenediyl_((C≦12)), or a substituted        version of any of these groups; and

n is an integer from 0-6.

In some embodiments, X is alkynediyl_((C2-8)), for example, —C≡C—. Insome embodiments, n is zero. In some embodiments, the linker is:

wherein

X is

-   -   —O—, —S—, or —NH—; or    -   alkanediyl_((C≦12)), alkenediyl_((C≦12)), alkynediyl_((C≦12)),        arenediyl_((C≦12)), heteroarenediyl_((C≦12)), or a substituted        version of any of these groups;

Y is —O—, —NH—, alkanediyl_((C≦12)) or substituted alkanediyl_((C≦12));

n is an integer from 0-6; and

m is an integer from 0-6.

In some embodiments, X is alkynediyl_((C2-8)), for example, —C≡C—. Insome embodiments, Y is —CH₂—. In some embodiments, n is zero. In someembodiments, m is zero. In some embodiments, the reporter is based on adye, wherein the dye is zanthene, fluorescein, rhodamine, BODIPY,cyanine, coumarin, pyrene, phthalocyanine, phycobiliprotein, or asquaraine dye. In some embodiments, the reporter is:

In some embodiments, R₆ is hydrogen. In some embodiments, the starredcarbon atom is in the S configuration. In some embodiments, the starredcarbon atom is in the R configuration. In some embodiments, the compoundis further defined as:

or a salt and/or protonated form of any of these formulas.

In some embodiments, the compound is further defined as:

wherein R is ═O or ═S, or a salt and/or protonated form of any of theseformulas.

In some embodiments, the compound is further as:

wherein R is ═O or ═S, or a salt and/or protonated form of any of theseformulas.

In some embodiments, the compound is further defined as:

or a salt and/or protonated form of any of these formulas.

In another aspect of the invention there are provided methods ofsequencing a target nucleic acid comprising the following steps:

-   -   (i) attaching the 5′-end of a primer to a solid surface;    -   (ii) hybridizing a target nucleic acid to the primer attached to        the solid surface to form a hybridized primer/target nucleic        acid complex;    -   (iii) obtaining a polymerase and one or more compounds described        herein, with the proviso that compound of different formulas        I-VII have different fluorophores;    -   (iv) reacting the hybridized primer/target nucleic acid complex        with a polymerase and one or more of the compounds of step (iii)        to form a growing primer strand via a polymerase reaction;    -   (v) imaging the growing primer strand to identify the        incorporated compound of step (iv) via its fluorophore;    -   (vi) exposing the solid surface with the growing primer strand        to a light source to remove a photocleavable terminating moiety        of the formula:

-   -   -   with the variables as defined herein referenced in step            (iii), resulting in an extended primer with            naturally-occurring components; and

    -   (vii) repeating steps (iv) through (vi) one or more times to        identify a plurality of bases in the target nucleic acid, where        the extended primer of step (vi) of the previous cycle reacts in        place of the hybridized primer/target nucleic acid complex in        step (iv) of the subsequent cycle.

In some embodiments, step (vi) is conducted in the presence of sodiumazide. In some embodiments, the sodium azide concentration is from 0.1mM to 10 mM, for examples, about 1 mM. In some embodiments, step (vi) isconducted in the presence of sodium acetate. In some embodiments, thesodium acetate concentration is from 0.1 mM to 10 mM, for example, about1 mM.

In some embodiments, steps (v) or (vi) is conducted in the presence ofthiourea. In some embodiments, the thiourea concentration is from 10 mMto 500 mM, for example, about 100 mM.

In some embodiments, step (vi) is conducted in the presence ofdithiothreitol (DTT).

In another aspect, there are provided methods of sequencing a targetnucleic acid comprising the following steps:

-   -   (i) attaching the 5′-end of a nucleic acid to a solid surface;    -   (ii) hybridizing a primer to the nucleic acid attached to the        solid surface to form a hybridized primer/target nucleic acid        complex;    -   (iii) obtaining a polymerase and one or more compounds described        herein, with the proviso that compound of different formulas        I-VII have different fluorophores    -   (iv) reacting the hybridized primer/target nucleic acid complex        with a polymerase and one or more of the compounds of step (iii)        to form a growing primer strand via a polymerase reaction;    -   (v) imaging the growing primer strand to identify the        incorporated compound of step (iv) via its fluorophore;    -   (vi) exposing the solid surface with the growing primer strand        to a light source to remove a photocleavable terminating moiety        of the formula:

-   -   -   with the variables as defined herein, resulting in an            extended primer with naturally-occurring components; and

    -   (vii) repeating steps (iv) through (vi) one or more times to        identify a plurality of bases in the target nucleic acid, where        the extended primer of step (vi) of the previous cycle reacts in        place of the hybridized primer/target nucleic acid complex in        step (iv) of the subsequent cycle.

In some embodiments, step (vi) is conducted in the presence of sodiumazide. In some embodiments, step (vi) is conducted in the presence ofdithiothreitol (DTT).

In some embodiments, the incorporation of at least one compoundaccording to step (iv) occurs at about 70% to about 100% of theefficiency of incorporation of its natural nucleotide counterpart. Insome embodiments, the incorporation efficiency occurs at about 85% toabout 100%.

In some embodiments, the polymerase is selected from the groupconsisting of reverse transcriptase, terminal transferase, and DNApolymerase. In some embodiments, about 85% to about 100% of thephotocleavable terminating moieties are removed by exposure to a lightsource in step (vi). In some embodiments, incorporation of at least onecompound according to step (iv) is followed by termination of strandgrowth at an efficiency of from about 90% to about 100%.

In some embodiments, a pulsed multiline excitation detector is used forimaging in step (v).

In some embodiments, the method further comprises washing the growingprimer strand prior after step (iv) or step (vi).

In some embodiments, the method further comprises, prior to step (iv),capping any primers or growing primer strands that did not react in step(iv).

In some embodiments, the method further comprises sequencing multipletarget nucleic acids synchronistically.

In another aspect of the invention, there are provided methods ofconverting a non-naturally occurring component in a nucleic acidmolecule into a naturally-occurring component comprising:

-   -   (i) incorporating a compound described herein;    -   (ii) exposing the resulting nucleic acid to a light source to        remove a photocleavable terminating moiety of the formula:

-   -   -   with the variables as defined herein, from the nucleic acid.

In some embodiments, the method further comprises convertingnon-naturally occurring components in multiple nucleic acid moleculesinto naturally-occurring components synchronistically. In someembodiments, the method further comprises terminating multiple nucleicacid syntheses synchronistically.

In another aspect, the invention provides methods of terminating anucleic acid synthesis comprising the step of placing a 3′-OH unblockednucleotide or nucleoside described above in the environment of apolymerase and allowing incorporation of the 3′-OH unblocked nucleotideor nucleoside into a nucleic acid molecule. In some embodiments,efficiency of termination of DNA synthesis upon incorporation of the3′-OH unblocked nucleotide or nucleoside ranges from about 90% to about100%. In some embodiments, the efficiency of incorporation of the 3′-OHunblocked nucleotide or nucleoside ranges from about 70% to about 100%compared to the efficiency of incorporation of a naturally-occurringnucleotide or nucleoside with the same base as the 3′-OH unblockednucleotide or nucleoside.

In another aspect, the invention provides methods of performing Sangeror Sanger-type sequencing comprising using a compound described hereinas a terminating nucleotide analog.

In another aspect, there are provided methods of determining thesequence of a target nucleic acid comprising

-   -   (i) adding a target nucleic acid to a Sanger or Sanger-type        sequencing apparatus,    -   (ii) adding one or more compounds described herein to the        sequencing apparatus, with the proviso that where more than one        type of base is present, each base is attached to a different        fluorophore;    -   (iii) adding a complementary primer and a polymerase enzyme,    -   (iv) performing a polymerase reaction to incorporate at least        one of the compounds of step (ii) into a growing nucleic acid        strand, and    -   (v) analyzing the result of the Sanger sequencing reaction with        fluorescence sequencing instrumentation or by pulsed multiline        excitation fluorescence,        wherein steps (i)-(iii) can be performed in any order.

In some embodiments, incorporation of at least one compound according tostep (iv) is followed by termination of strand growth at an efficiencyof from about 90% to about 100%. In some embodiments, the incorporationof at least one compound according to step (iv) occurs at about 70% toabout 100% of the efficiency of incorporation of a native substrate withthe same base in the polymerase reaction. In some embodiments, theincorporation efficiency occurs at about 85% to about 100%. In someembodiments, the polymerase is selected from the group consisting ofreverse transcriptase, terminal transferase, and DNA polymerase.

In another aspect, the invention provides methods of incorporating anon-naturally occurring component into a nucleic acid comprising:

-   -   (i) adding a target nucleic acid to a sequencing apparatus;    -   (ii) adding one or more compounds described herein to the        sequencing apparatus, with the proviso that where more than one        type of base is present, each base is attached to a different        fluorophore;    -   (iii) adding a polymerase enzyme; and    -   (iv) performing a polymerase reaction to incorporate at least        one of the compounds of step (ii) into a growing nucleic acid        strand,        wherein steps (i)-(iii) can be performed in any order.

In some embodiments, the method further comprises:

-   -   (v) analyzing the result of the polymerase chain reaction for        incorporation of at least one compound from step (ii).

In some embodiments, incorporation of at least one compound according tostep (iv) is followed by termination of strand growth at an efficiencyof from about 90% to about 100%. In some embodiments, the incorporationof at least one compound according to step (iv) occurs at about 70% toabout 100% of the efficiency of incorporation of native substrate withthe same base in the polymerase reaction a native substrate with thesame base in the polymerase reaction.

In another aspect, the invention provides methods of performingmini-sequencing or minisequencing-type sequencing comprising addition ofa compound described herein to a mini-sequencing or minisequencing-typesequencing method.

In some embodiments of any of the methods described above, the compoundis further defined as a compound of formula I, II, III, IV, V, VI, orVII.

In another aspect, the invention provides a system comprising:

-   -   a flowcell comprising a plurality of beads, wherein:        -   each bead attached to a DNA molecule, wherein a compound            described herein has been incorporated into using a            polymerase; and        -   the flowcell is at least partially transparent to visible            and UV light;    -   an imaging device configured to capture images of the flowcell;    -   a filter wheel comprising at least four spectral filters,        wherein the filter wheel is configured to cycle between each        filter;    -   a lamp configured to create a light path from the flowcell        through a filter in the filter wheel to the imaging device; and    -   an ultraviolet light source configured to provide ultraviolet        light to the DNA molecules on the flowcell.

In some embodiments, the flowcell is a microfluidic flowcell. In someembodiments, the system further comprises an objective lens between thefilter wheel and the flowcell. In some embodiments, the system furthercomprises a mirror configured to direct the light path to the imagingdevice.

In some aspects, the present disclosure provides for cancer diagnosticsthat are fast, high-throughput, accurate and sensitive for early-stagedetection to identify rare sequence variants that belong to a limitedsubpopulation of cells undergoing a cancerous transformation.

Other objects, features and advantages of the present disclosure willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating specific embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.Note that simply because a particular compound is ascribed to oneparticular generic formula does not mean that it cannot also belong toanother generic formula.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentdisclosure. The invention may be better understood by reference to oneof these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1—Structures of 2-Nitrobenzyl Alkylated HOMedNTP Analogs. “R” is H,iso-propyl, or tert-butyl. “R”′ is H, 4-OMe, 5-OMe, 4,5-di-OMe, or6-NO₂. See keys for specific examples. “*” denotes two differentstereochemical configurations at this carbon atom. The portion of theformulas within the dashed ellipsoids highlights the terminatingfunctional groups that are cleaved upon exposure to UV light.

FIG. 2—Elimination of Transient Product (TP) with DTT. Fluorescent gelimage of UV photochemical cleavage time series of dU.VI incorporated byTherminator polymerase in the presence of (A) 1 mM NaN₃ and (B) 1 mMNaN₃, 50 mM DTT. Lanes: “P” (primer) contains Therminator bound tooligoTemplate-4 hybridized with BODIPY-FL labeled primer-1 in 1×ThermoPol buffer (Wu et al., 2007; Litosh et al., 2011), “I”(incorporation) contains that found in lane “P” plus 100 nM dU.VI, andtime point lanes contain that found in lane “I” plus listed timessamples were exposed to 0.70 W/cm² 365 nm light. “IP” denotesincorporated product and “P” denotes cleaved product.

FIG. 3—X-ray Crystal Structure of(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl (1S)-camphanate.Crystallographic measurements were made on a crystal of(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl (1S)-camphanatewith dimensions of 0.50 mm×0.05 mm×0.05 mm as described in Litosh et al.(2011), which is incorporated herein by reference. Data collection: CuKαradiation, λ=1.54178 Å, T=110±2° K, 2θ_(max)=120.0°, 32,513 reflectionscollected, 2,913 unique (R_(int)=0.0517). Final GooF=1.091, R1=0.0681,wR2=0.1695, R indices based on 2,913 reflections with I>2sigma(I)(refinement on F²), 290 parameters, 43 restraints. Lp and absorptioncorrections applied, μ0.819 mm⁻¹. Absolute structure parameter:0.05±0.09. X-Ray crystallography data: C₂₂H₂₉NO₇, M=419.46.Orthorhombic, a=6.29, b=15.00, c=22.27 Å (α, β, γ32 90°), V=2,099.29 Å³,space group P2₁2₁2₁, Z=4, D_(c)=1.327 g/cm⁻³, F(000)=896.

FIG. 4—DTT Eliminates the Nitroso Intermediate (TP). Fluorescent gelimage of UV photochemical cleavage experiment of dU.VI incorporated byTherminator™ polymerase. Lanes: “P” (primer) contains Therminator™ boundto oligoTemplate-4 hybridized with BODIPY-FL labeled primer-1 in 1×ThermoPol buffer, “I” (incorporation) contains that found in lane “P”plus 100 nM dU.VI. Reagents A-G listed as final concentrations in thekey were added, and samples were exposed to 0.70 W/cm² 365 nm light for10 sec. “IP” denotes incorporated product, “P” denotes cleaved product,and “TP” denotes transient product.

FIGS. 5A & B—Optical Set-Up for UV Photochemical Cleavage Measurements.FIG. 5A shows a schematic of the modified 0.5 mL Eppendorf tube cut inhalf, PM100 power meter, a 1,000 μm pinhole cassette using a 3-axismanual translation stage to align the arc beam. FIG. 5B shows a sampleholder and modified 0.5 mL Eppendorf tube with an internal alignmentcard to align the arc beam to the center of a 10 μL or 20 μL reactionsample.

FIG. 6—Example of photochemical cleavage reaction. Upon UV-inducedphotochemical cleavage, the terminating 2-nitrobenzyl derivative isreleased to yield a natural hydroxymethyl nucleotide. The combination ofa stereospecific (S)-tert-butyl group attached at the benzylic carboncoupled with a 5-OMe group modified on the 2 nitrobenzyl ringsubstantially increased the rate of the photochemical cleavage reaction.For the case of C⁷-HOMedG, the rate increased by more than one order ofmagnitude over its corresponding parent analog.

FIG. 7—tert-Butyl Substitution at the α-Carbon and Methoxy Substitutionat the 5 Position Correlates with Improved Photochemical Cleavage Rates.This figure compares photochemical cleavage rates of the parent,(S)-α-tert-butyl, and (S)-α-tert-butyl-5-OMe 2-nitrobenzyl groupsalkylated on C⁷-HOMedA, HOMedC, C⁷-HOMedG, and HOMedU nucleosides. LowerDT₅₀ values indicate faster photochemical cleavage rates.

FIG. 8. A schematic representation of a system for imaging fluorescentbeads on a flowcell.

FIG. 9—Example of Bead Preparation and Immobilization Method. Schematicillustration of the steps of an exemplary mpreparing a bead sample on aflowcell.

FIG. 10. Schematic illustration of the steps of incorporation,fluorescence imaging, and photochemical cleavage in a CRT cycle.

FIG. 11. Illustration of tile images from three CRT cycles andsubsequent base-calling from individual beads.

FIG. 12—Chemical Formulas of 3′-OH Reversible Terminators Attached toGeneric Dyes (“Fluor”). The portion of the formulas encompassed by thedashed ellipsoid denotes the dye-labeled terminating functional groupsand that are cleaved upon exposure to UV light.

FIG. 13—Diagram of the Random Nick Sequencing (RNS) method. LightningTerminators™ denoted in the figure are comprised of the reversibleterminators of the present invention.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS I. Reversible Terminators andMethods of Synthesis Thereof

In one aspect, the present disclosure provides new compounds that may beused to function as reversible terminators in a variety of different DNAsequencing applications. The compounds provided by the presentdisclosure are also referred to as reversible terminators, 3′-OHunblocked reversible terminators, and as Lightning Terminators™. In someembodiments, compounds of the following formulas are provided:

wherein:

-   -   R₁ is hydroxy, monophosphate, diphosphate, triphosphate,        α-thiotriphosphate or polyphosphate;    -   R₂ is hydrogen or hydroxy;    -   R₃ is alkyl_((C≦8)) or substituted alkyl_((C≦8));    -   R₄ is        -   hydrogen, hydroxy, halo, amino, nitro, cyano, azido or            mercapto;        -   alkyl_((C≦6)), acyl_((C≦6)), alkoxy_((C≦6)),            acyloxy_((C≦6)), alkylamino_((C≦6)), dialkyl-amino_((C≦6)),            amido_((C≦6)), or a substituted version of any of these            groups;    -   R₅ and R₆ are each independently:        -   hydrogen, hydroxy, halo, amino, nitro, cyano, azido or            mercapto;        -   alkyl_((C≦6)), alkenyl_((C≦6)), alkynyl_((C≦6)),            aryl_((C≦6)), aralkyl_((C≦8)), heteroaryl_((C≦6)),            acyl_((C≦6)), alkoxy_((C≦6)), acyloxy_((C≦6)),            alkylamino_((C≦6)), dialkyl-amino_((C≦6)), amido_((C≦6)), or            a substituted version of any of these groups;        -   a group of formula:

-   -   -   -   wherein                -   X is                -    —O—, —S—, or —NH—; or                -    alkanediyl_((C≦12)), alkenediyl_((C≦12)),                    alkynediyl_((C≦12)), or a substituted version of any                    of these groups;                -   Y is —O—, —NH—, alkanediyl_((C≦12)) or substituted                    alkane-diyl_((C≦12));                -   n is an integer from 0-6; and                -   m is an integer from 0-6; or

        -   a -linker-reporter;            or a salt, tautomer, or optical isomer thereof

Dye-labeled α-tBu-5-OMe-2-nitrobenzyl alkylated hydroxymethylnucleotides may be synthesized according to the following schemes andprocedures.

A. Synthesis of dye labeled7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphates

B. Synthesis of dye labeled5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine-5′-triphosphate

C. Synthesis of dye labeled7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

D. Synthesis of dye labeled5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine-5′-triphosphate

In some embodiments, it was observed that the stereochemistry of thealkyl substituted at the α-carbon can improve the photochemical cleavageproperties of a 2-nitrobenyl group. In some embodiments, it was observedthat faster photochemical cleavage rates result by combining thestereospecific group at the α-carbon with another chemical groupattached to the 2-nitrobenzyl ring. See, for example, FIG. 7.

Compounds of the present disclosure may be made using the methodsdescribed above and in the Example section below. For example, a summaryof a synthesis for making α-tBu-5-OMe-2-nitrobenzyl alcohol, includingan enantiopure form thereof, is provided in Example 8. These methods canbe further modified and optimized using the principles and techniques oforganic chemistry as applied by a person skilled in the art. Suchprinciples and techniques are taught, for example, in March's AdvancedOrganic Chemistry: Reactions, Mechanisms, and Structure (2007), which isincorporated by reference herein.

Compounds employed in methods of the invention may contain one or moreasymmetrically-substituted carbon or nitrogen atoms, and may be isolatedin optically active or racemic form. Thus, all chiral, diastereomeric,racemic form, epimeric form, and all geometric isomeric forms of astructure are intended, unless the specific stereochemistry or isomericform is specifically indicated. Compounds may occur as racemates andracemic mixtures, single enantiomers, diastereomeric mixtures andindividual diastereomers. In some embodiments, a single diastereomer isobtained. The chiral centers of the compounds of the present inventioncan have the S or the R configuration. For example, in some aspects ofthe present disclosure, substitution and its stereochemistry of theα-carbon of the benzyl ether of modified 5-hydroxymethyl pyrimidine or7-hydroxymethyl-7-deazapurine bases affects biological function andcleavage rates of reaction of 3′-OH unblocked, base-modified dNTPs.

Compounds of the invention may also have the advantage that they may bemore efficacious than, be less toxic than, be longer acting than, bemore potent than, produce fewer side effects than, be more easilyabsorbed than, and/or have a better pharmacokinetic profile (e.g.,higher oral bioavailability and/or lower clearance) than, and/or haveother useful pharmacological, physical, or chemical properties over,compounds known in the prior art, whether for use in the indicationsstated herein or otherwise.

Chemical formulas used to represent compounds of the invention willtypically only show one of possibly several different tautomers. Forexample, many types of ketone groups are known to exist in equilibriumwith corresponding enol groups. Similarly, many types of imine groupsexist in equilibrium with enamine groups. Regardless of which tautomeris depicted for a given compound, and regardless of which one is mostprevalent, all tautomers of a given chemical formula are intended.

In addition, atoms making up the compounds of the present invention areintended to include all isotopic forms of such atoms. Isotopes, as usedherein, include those atoms having the same atomic number but differentmass numbers. By way of general example and without limitation, isotopesof hydrogen include tritium and deuterium, and isotopes of carboninclude ¹³C and ¹⁴C. Similarly, it is contemplated that one or morecarbon atom(s) of a compound of the present invention may be replaced bya silicon atom(s). Furthermore, it is contemplated that one or moreoxygen atom(s) of a compound of the present invention may be replaced bya sulfur or selenium atom(s).

In some embodiments, the 3′-OH unblocked reversible terminators providedherein have an alpha-thiophosphate group, preferably analpha-thiotriphosphate group. See, for example, compounds 54b, 55b, 59b,60b, 63b, 64b, 68b, and 69b, in Example 8 below. It is well known in theart that DNA polymerases exhibit 3′-5′ exonuclease activity. Thefunction of the 3′-5′ exonuclease activity is to remove the justincorporated nucleotide from the primer strand. Many commerciallyavailable DNA polymerases delete or mutate the 3′-5′ exonuclease domainto reduce this activity below detectable levels. Nonetheless, even lowlevel activity of some DNA polymerases can result in poor sequence dataquality due to dephasing of the primary signal. In some embodiments, the3′-OH unblocked reversible terminators having alpha-thiotriphosphategroups may be used to reduce, minimize and/or eliminate the residual3′-5′ exonuclease activity. Without being bound by theory, it is wellknown in the art that alpha-thiotriphosphates are resistant toexonuclease activity. See, for example, European Patent EP 0 640 146 toRosenthal and Brenner, which is incorporated herein by reference.

Compounds of the present invention may also exist in prodrug form. Sinceprodrugs are known to enhance numerous desirable qualities ofpharmaceuticals (e.g., solubility, bioavailability, manufacturing,etc.), the compounds employed in some methods of the invention may, ifdesired, be delivered in prodrug form. Thus, the invention contemplatesprodrugs of compounds of the present invention as well as methods ofdelivering prodrugs. Prodrugs of the compounds employed in the inventionmay be prepared by modifying functional groups present in the compoundin such a way that the modifications are cleaved, either in routinemanipulation or in vivo, to the parent compound. Accordingly, prodrugsinclude, for example, compounds described herein in which a hydroxy,amino, or carboxy group is bonded to any group that, when the prodrug isadministered to a subject, cleaves to form a hydroxy, amino, orcarboxylic acid, respectively.

The present disclosure further provides nucleotide and nucleosidecompounds as well as salts, esters and phosphates thereof, that can beused in rapid DNA sequencing technology. However, it should berecognized that the particular anion or cation forming a part of anysalt of this invention is not critical, so long as the salt, as a whole,is pharmacologically acceptable. Additional examples of pharmaceuticallyacceptable salts and their methods of preparation and use are presentedin Handbook of Pharmaceutical Salts: Properties, and Use (2002), whichis incorporated herein by reference. The compounds are optionally in theform of ribonucleoside triphosphates (NTPs) and deoxyribonucleosidetriphosphates (dNTP). The nucleotide and nucleoside compounds in somecases include a chemically or enzymatically cleavable group labeled witha reporter group such as a fluorescent dye. The nucleotide andnucleoside compounds include chemically or enzymatically removableprotecting groups that are designed to terminate DNA synthesis as wellas cleave rapidly, so that these monomers can be used for rapidsequencing in a parallel format. The presence of such rapidly cleavablegroups labeled with fluorescent dyes on the nucleotide and nucleosidecompounds can enhance the speed and accuracy of sequencing of largeoligomers of DNA in parallel, to allow, for example, rapid whole genomesequencing, and the identification of polymorphisms and other valuablegenetic information.

These 3′-OH unblocked terminators are well-tolerated by a number ofcommercially available DNA polymerases, representing a key advantageover 3′-O-blocked terminators. The benzyl group of the compoundsdisclosed herein can also can be derivatized to include a selectedfluorescent dye or other reporter group.

II. Properties of Reversible Terminators

As discussed above, in one aspect, there are provided novel alkylated2-nitrobenzyl nucleotides with fast photochemical cleavage propertiesthat may be used as improved reversible terminators for cyclicreversible terminator (CRT) sequencing applications. Such applicationsare described in Metzker (2005, 2010), which are both incorporated byreference herein. In some embodiments, there are provided modified7-deaza-7-hydroxymethyl-2′-deoxyadenosine (C⁷-HOMedA) (Rockhill et al.,1997) and 7-deaza-7-hydroxymethyl-2′-deoxyguanosine (C⁷-HOMedG)(McDougall et al., 2001) along with HOMedC and HOMedU with a variety ofsubstituted 2-nitrobenzyl groups. See FIG. 1. In some embodiments, thereversible terminators disclosed herein exhibit a number of suitableproperties, including fast kinetics of nucleotide incorporation,single-base termination, high nucleotide selectivity, and/or rapidcleavage of the terminating group.

Chromatographic conditions were identified to separate C⁷-HOMedA analogsinto single diastereomeric nucleotides, with the first eluting isomerdenoted as ds1 and the second as ds2. To evaluate the photochemicalcleavage effect of the stereochemistry of an α-isopropyl groupsubstitution with the 2-nitrobenzyl ring modifications of 4-methoxy(4-OMe) and 6-nitro (6-NO₂), three C⁷-HOMedA analogs dA.III.a-dA.III.c,were synthesized, as well as the parent dA.I (see Examples sectionbelow). Incorporation assays were performed with these 2-nitrobenzylalkylated C⁷-HOMedATP analogs and then subjected to UV photochemicalcleavage experiments in sodium azide solution (Table 1).

TABLE 1 Photochemical Cleavage Rates of C⁷-HOMedA Analogs DT₅₀ in 1 mMNaN₃ C⁷-HOMedA analog No DTT 50 mM DTT dA.I 3.6 ± 0.1 3.5 ± 0.1 dA.III.ads1 4.5 ± 0.2 4.4 ± 0.2 dA.III.a ds2 2.2 ± 0.1 2.1 ± 0.1 dA.III.b ds17.0 ± 0.3 6.1 ± 0.4 dA.III.b ds2 1.1 ± 0.1 1.0 ± 0.1 dA.III.c ds1 3.4 ±0.2 3.0 ± 0.2 dA.III.c ds2 2.8 ± 0.2 2.5 ± 0.1

In all cases, the ds2 isomers of dA.III.a-dA.III.c showed fasterphotochemical cleavage rates (i.e., lower DT₅₀ values) by factors of2.0×, 6.4×, and 1.2×, respectively, compared with those of their ds1counterparts. Interestingly, the ds1 isomers exhibited similar(dA.III.c) or higher (dA.III.a or dA.III.b) DT₅₀ values compared withthe parent dA.I analog. These data provide evidence that stereochemistryof the substituted α-isopropyl group is an important determinant, andcoupled with a 4-OMe substitution, the dA.III.b ds2 analog produced thelowest DT₅₀ value for the α-isopropyl C⁷-HOMedA set.

Previous work demonstrated that the α-tert-butyl analog dU.V exhibitedexcellent CRT properties such as single-base termination and highnucleotide selectivity (Litosh et al., 2011). This allowed to furtherexamination of the stereospecific effect using a differentα-substitution group coupled with various OMe ring substitutions bysynthesizing four α-tert-butyl C⁷-HOMedG analogs, dG.V.a-dG.V.d, alongwith the parent dG.I (FIG. 1). Consistent with theα-isopropyl-C⁷-HOMedATP analogs, UV photochemical cleavage experimentsrevealed that ds2 isomers of dG.V.a-dG.V.d showed faster rates byfactors of 3.1×, 4.5×, 4.4×, and 3.0×, respectively, compared with thoseof their ds1 counterparts (Table 2).

TABLE 2 Photochemical Cleavage Rates of C⁷-HOMedG Analogs. DT₅₀ in 1 mMNaN₃ C⁷-HOMedG analog No DTT 50 mM DTT dG.I 9.2 ± 0.3 8.1 ± 0.2 dG.V.ads1 11.0 ± 0.4  10.7 ± 0.2  dG.V.a ds2 3.6 ± 0.3 3.5 ± 0.3 dG.V.b ds14.9 ± 0.3 4.6 ± 0.3 dG.V.b ds2 1.1 ± 0.1 1.3 ± 0.2 dG.V.c ds1 3.5 ± 0.33.0 ± 0.1 dG.V.c ds2 0.8 ± 0.1 0.8 ± 0.1 dG.V.d ds1 2.4 ± 0.1 2.3 ± 0.2dG.V.d ds2 0.8 ± 0.1 0.8 ± 0.1

Both 5-OMe ds1 and ds2 isomers exhibited faster photochemical cleavagerates of 1.4× fold each compared with the corresponding 4-OMe isomers.The bis-substituted 4,5-di-OMe ds1 isomer showed faster cleavage ratescompared with mono-substituted 4-OMe (2.0×) or 5-OMe (1.5×) isomers.Conversely, the 5-OMe ds2 and 4,5-di-OMe ds2 isomers exhibited identicalDT₅₀ values of just 0.8 sec. In the absence of an α-substitution group,Hasan et al. (1997) reported a rate increase of only 1.2× for a5-OMe-2-nitrobenzyl analog over its corresponding parent. Comparison ofds1 and ds2 isomers of dG.V.c with dG.V.a revealed higher rate increasesof 3.6× and 4.4×, respectively, suggesting that the stereospecifictert-butyl group enhances the effect of the 5-OMe group. With four-colorCRT applications, this combination provides good flexibility in ringsystem utility, as a linker structure can also be attached to the4-position to create dye-labeled analogs (U.S. Pat. Nos. 7,897,7377,964,352, and 8,148,503; U.S. Patent Appl. Publication 2011/0287427;Metzker, 2010).

To determine the stereochemistry of these α-tert-butyl C⁷-HOMedGanalogs, the (1S)-camphanate of(R/S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol was resolvedinto its enantiopure (S) alcohol by fractional crystallization (Corrieet al., 1992) (FIG. 3). This (S) alcohol and(S)-α-tert-butyl-2-nitrobenzyl alcohol (U.S. Pat. No. 8,148,503; Litoshet al., 2011) were each coupled to C⁷-HOMedG (FIG. 1). RP-HPLC analysisof their corresponding triphosphates revealed that both ds2 isomers ofdG.V.a and dG.V.c had identical peak retention times as that for dG.Vand dG.VI, respectively, thus allowing us to determine that both ds2isomers have the same (S) configuration at the α-carbon. By inference,the corresponding ds1 isomers of dG.V.a and dG.V.c have been assignedthe (R) configuration.

These (S) alcohols were then coupled to the remaining nucleosides toexamine the effect of the leaving group on the photochemical cleavagerate. For example, UV photochemical cleavage experiments revealed thatDT₅₀ values for the parent 2-nitrobenzyl analogs varied from 2.0 sec fordC.I to 9.2 sec for dG.I (FIG. 7 and Table 3).

TABLE 3 Photochemical Cleavage Rates of Reversible Terminators DT₅₀ in 1mM NaN₃ Nucleotide analog No DTT 50 mM DTT dA.I 3.6 ± 0.1 3.5 ± 0.1 dA.V2.1 ± 0.1 2.0 ± 0.2 dA.VI  0.8 ± 0.1^([a]) 0.8 ± 0.1 dC.I 2.0 ± 0.3 1.6± 0.2 dC.V 1.2 ± 0.1 1.0 ± 0.2 dC.VI  0.6 ± 0.1^([a]) 0.6 ± 0.1 dG.I 9.2± 0.3 8.1 ± 0.2 dG.V 3.0 ± 0.1 2.9 ± 0.2 dG.VI 0.8 ± 0.1 0.8 ± 0.1 dU.I2.1 ± 0.1 1.7 ± 0.1 dU.V 1.4 ± 0.1 1.3 ± 0.1 dU.VI  0.7 ± 0.1^([a]) 0.7± 0.1 ^([a])Transient product (TP) observed by gel electrophoresis;considered as cleaved product in DT₅₀ value.

Substitution of the benzylic carbon with (S)-tert-butyl resulted inincreased cleavage rates by factors of 1.5×-3.1× and the additionalsubstitution with a 5-OMe group further increased rates by factors of3.0×-11.5× compared with the parent analogs. The greatest rateimprovement was observed when comparing C⁷-HOMedG analogs, reducing DT₅₀values from 9.2 to 0.8 sec (FIG. 7, black bars). The complete set of(S)-5-OMe-α-tert-butyl reversible terminators showed a more narrow rangeof DT₅₀ values from 0.6 to 0.8 sec. These data suggest that the combinedeffects of the (S)-α-tert-butyl and 5-OMe groups play an important rolein diminishing cleavage rate variation observed with particularnucleotide leaving groups, having the practical application of providingnormalized and faster cleavage conditions for the CRT cycle.Unexpectedly, transient products were observed from incorporation assaysfor (S)-5-OMe-α-tert-butyl-C⁷-HOMedA, -HOMedC and -HOMedU, but not—C⁷-HOMedG, following brief exposure to UV light (HOMedU only shown inFIG. 2, left side). As the only difference being the just incorporatednucleotide, we hypothesize that the faster cleaving(S)-5-OMe-α-tert-butyl-2-nitrobenzyl group produces a more reactive2-nitrosoketone by-product that attacks the 3′-terminal nucleotide ofthe growing primer strand.

To investigate conditions to quench the nitroso intermediate, a numberof amino and thiol agents were tested during UV photochemical cleavageexperiments (FIG. 5). Of these, only dithiothreitol (DTT) (Cleland,1964) eliminated the transient product (FIG. 2, right side). In someembodiments, the effective DTT concentration is from 1 mM to 1 M. Insome embodiments, the effective DTT concentration is from 5 mM to 100mM. In some embodiments, the effective DTT concentration is from 10 mMto 50 mM. In some embodiments, the effective DTT concentration is about50 mM. In some embodiments, the photochemical cleavage step takes placein the presence of sodium azide. In some embodiments, the effectivesodium azide concentration is from 0.1 mM to 1 M. In some embodiments,the effective sodium azide concentration is from 1 mM to 100 mM. In someembodiments, the effective sodium azide concentration is from 1 mM to 50mM. In some embodiments, the effective sodium azide concentration isabout 1 mM.

To test rate effects, UV photochemical cleavage experiments wererepeated for all compounds in the presence of DTT, of which DT₅₀ valuesfor several parent and ds1 isomers were reduced (Tables 1, 2, and 3).Barth et al. (2005) proposed that DTT attacks the nitroso group bynucleophilic addition, although a later review by Corrie (2005)describes protective thiols as unnecessary as the evidence forbiological interference from of the nitrosoketone by-product remainsminimal. In our examples described in this invention, DTT plays animportant protective role against such undesired reactions.

The stereospecific (S) configuration of the α-substituted group combinedwith a 5-methoxy group were found to be determinants in creatingfast-cleaving reversible terminators. The reactive nitrosoketoneby-product can be effectively eliminated during photochemical cleavagein the presence of DTT, providing appropriate conditions in maintainingthe biological integrity of the CRT reaction.

III. Nucleotide and Nucleoside Compounds and their Use in DNA Sequencing

The reversible terminators of the present invention may be used in DNAsequencing methods based on a variety of approaches, including:

-   -   “Sanger” or “dideoxy” methods, which involve the chain        termination of DNA synthesis by the incorporation of        2′,3′-dideoxynucleotides (ddNTPs) using DNA polymerase. See        Metzker et al., 2005, which is incorporated herein by reference.    -   Sequencing-by-synthesis (SBS), which typically does not clearly        delineate the different mechanics of sequencing DNA. See        Metzker, 2010; Metzker 2005, which are incorporated herein by        reference.    -   DNA polymerase-dependent strategies, which are also classified        as cyclic reversible termination (CRT), single nucleotide        addition (SNA, e.g., pyrosequencing), and real-time sequencing.        See Metzker, 2010, which is incorporated herein by reference.    -   Single molecules sequencing using the Random Nick Sequencing        (RNS) approach.

In some embodiments, the invention provides methods of sequencing atarget nucleic acid comprising the following steps:

-   -   (i) attaching the 5′-end of a primer to a solid surface;    -   (ii) hybridizing a target nucleic acid to the primer attached to        the solid surface;    -   (iii) adding a compound according to any of structures described        herein, with the proviso that where more than one type of base        is present, each base is attached to a different reporter group;    -   (iv) adding a nucleic acid replicating enzyme to the hybridized        primer/target nucleic acid complex to incorporate the        composition of step (iii) into the growing primer strand,        wherein the incorporated composition of step (iii) terminates        the polymerase reaction at an efficiency of between about 70% to        about 100%;    -   (v) washing the solid surface to remove unincorporated        components;    -   (vi) detecting the incorporated reporter group to identify the        incorporated composition of step (iii);    -   (vii) optionally adding one or more chemical compounds to        permanently cap unextended primers;    -   (viii) removing the terminating moiety comprising        photochemically cleaving off the terminating moiety, resulting        in an extended primer with 5-hydroxymethyl pyrimidine or        7-hydroxymethyl-7-deazapurine bases;    -   (ix) washing the solid surface to remove the cleaved terminating        group; and    -   (x) repeating steps (iii) through (viii) one or more times to        identify the plurality of bases in the target nucleic acid.        In some variations, the order of steps (iii) and (iv) is        reversed. In further variations, the polymerase and the compound        are added at the same time. In embodiments, they are in the same        solution.

In another aspect the invention provides a method of sequencing a targetnucleic acid comprising the following steps:

-   -   (i) attaching the 5′-end of a target nucleic acid to a solid        surface;    -   (ii) hybridizing a primer to the target nucleic acid attached to        the solid surface;    -   (iii) adding a compound according to any of structures described        herein, with the proviso that where more than one type of base        is present, each base is attached to a different reporter group;    -   (iv) adding a nucleic acid replicating enzyme to the hybridized        primer/target nucleic acid complex to incorporate the        composition of step (iii) into the growing primer strand,        wherein the incorporated composition of step (iii) terminates        the polymerase reaction at an efficiency of between about 70% to        about 100%;    -   (v) washing the solid surface to remove unincorporated        components;    -   (vi) detecting the incorporated reporter group to identify the        incorporated composition of step (iii);    -   (vii) optionally adding one or more chemical compounds to        permanently cap unextended primers;    -   (viii) removing the terminating moiety comprising        photochemically cleaving off the terminating moiety, resulting        in an extended primer with a 5-hydroxymethyl pyrimidine or        7-hydroxymethyl-7-deazapurine bases;    -   (ix) washing the solid surface to remove the cleaved terminating        group; and    -   (x) repeating steps (iii) through (ix) one or more times to        identify the plurality of bases in the target nucleic acid.        In some variations, the order of steps (iii) and (iv) is        reversed.

In some embodiments the compound is incorporated by a nucleic acidreplicating enzyme that is a DNA polymerase. In some embodiments the DNApolymerase is selected from the group consisting of Taq DNA polymerase,Klenow(exo-) DNA polymerase, Bst DNA polymerase, VENT® (exo-) DNApolymerase (DNA polymerase A cloned from Thermococcus litoralis andcontaining the D141A and E143A mutations), Pfu(exo-) DNA polymerase, andDEEPVENT™ (exo-) DNA polymerase (DNA polymerase A, cloned from thePyrococcus species GB-D, and containing the D141A and E143A mutations).In some embodiments the DNA polymerase is selected from the groupconsisting of AMPLITAQ® DNA polymerase, FS (Taq DNA polymerase thatcontains the G46D and F667Y mutations), THERMOSEQUENASE™ DNA polymerase(Taq DNA polymerase that contains the F667Y mutation), THERMOSEQUENASE™II DNA polymerase (blend of THERMOSEQUENASE™ DNA polymerase and T.acidophilum pyrophosphatase), THERMINATOR™ DNA polymerase (DNApolymerase A, cloned from the Thermococcus species 9° N-7 and containingthe D141A, E143A and A485L mutations), THERMINATOR™ II DNA polymerase(THERMINATOR™ DNA polymerase that contains the additional Y409Vmutation), and VENT® (exo-) A488L DNA polymerase (VENT® (exo-) DNApolymerase that contains the A488L mutation).

Compounds of the present disclosure may be made using the methodsoutlined in the Examples section. These methods can be further modifiedand optimized using the principles and techniques of organic chemistryas applied by a person skilled in the art. Such principles andtechniques are taught, for example, in Wu et al. (2007; Litosh et al.(2011); Stupi et al. (2012); Gardner et al., 2012; U.S. Pat. Nos.7,897,737, 7,964,352, and 8,148,503; U.S. Patent Appl. Publ.2011/0287427, which is incorporated herein by reference.

In some embodiments, sample components enable the determination of SNPs.The method may be for the high-throughput identification of informativeSNPs. The SNPs may be obtained directly from genomic DNA material, fromPCR amplified material, or from cloned DNA material and may be assayedusing a single nucleotide primer extension method. The single nucleotideprimer extension method may comprise using single unlabeled dNTPs,single labeled dNTPs, single 3′-O-modified dNTPs, single base-modified2′-dNTPs, single alpha-thio-dNTPs or single labeled2′,3′-dideoxynucleotides. The mini-sequencing method may comprise usingsingle unlabeled dNTPs, single labeled dNTPs, single 3′-O-modifieddNTPs, single base-modified 2′-dNTPs, single alpha-thio-dNTPs or singlelabeled 2′,3′-dideoxynucleotides. The SNPs may be obtained directly fromgenomic DNA material, from PCR amplified material, or from cloned DNAmaterials.

A. Nucleotide and Nucleoside Compounds and their Use in CRT

In some aspects of the present invention, nucleotide and nucleosidecompounds provided herein (reversible terminators) may be used in DNAsequencing technology based on cyclic reversible termination (CRT). CRTis a cyclic method of detecting the synchronistic, single base additionsof multiple templates. This approach differentiates itself from theSanger method (Metzker, 2005, which is incorporated herein by reference)in that it can be performed without the need for gel electrophoresis, amajor bottleneck in advancing this field. Like Sanger sequencing,however, longer read-lengths translates into fewer sequencing assaysneeded to cover the entire genome. The CRT cycle typically comprisesthree steps, incorporation, imaging, and deprotection. The term“deprotection” may be used synonymously with “cleavage”, so that thethree steps could also be described as incorporation, imaging, andcleavage. For this procedure, cycle efficiency, cycle time, andsensitivity are important factors. The cycle efficiency is the productof deprotection and incorporation efficiencies and determines the CRTread-length. The CRT cycle time is the sum of incorporation, imaging,and deprotection times. For rapid CRT for whole genome sequencing, thenucleotide and nucleoside compounds as disclosed herein may be used,which can exhibit fast and efficient deprotection properties. Thesecompounds can be labeled with reporter groups such as fluorescent dyes,attached directly to the benzyl group having an azido substitution onthe alpha carbon, providing, e.g., fluorescent, reversible terminatorswith similar deprotection properties. It has remained difficult toaccomplish the goal of long CRT reads because reversible terminatorstypically act as poor substrates with commercially available DNApolymerases. Modified nucleotide analogs of the present invention may beused to improve this technology by providing substrates that incorporateas well or better than a natural nucleotide with commercially availableDNA polymerases.

Photocleavable groups attached to the base of a 3′-OH unblockednucleotide, such as the groups described herein, can act as an effectivereversible terminator and be efficiently incorporated by wild-type DNApolymerases. See Wu et al., 2007; Metzker, 2010; Litosh et al., 2011;Gardner et al., 2012; U.S. Pat. Nos. 7,897,737, 7,964,352, and8,148,503; U.S. Patent Appl. Publ. 2011/0287427, which are incorporatedherein by reference. For example, 5-hydroxymethyl-2′-deoxyuridine(HOMedU) is found naturally in the genomes of numerous bacteriophagesand lower eukaryotes (Gommers-Ampt, 1995, which is incorporated hereinby reference). Its hydroxymethyl group can serve as molecular handle toattach a small photocleavable terminating group. Other naturallyoccurring hypermodified bases that can be further modified in the mannerdescribed herein to function as reversible terminators include5-hydroxymethyl-2′-deoxycytidine (HOMedC), which is found naturally inthe genomes of T2, T4, and T6 bacteriophages (Wyatt & Cohen, 1953;Gommers-Ampt, 1995) and of mammals (Kriaucionis & Heintz, 2009;Tahiliani et al., 2009; Ito et al., 2010). The pyrrolopyrimidine ringstructure (7-deazapurine) is also found naturally in nucleosideantibiotics (Carrasco & Vázquez, 1984, which is incorporated herein byreference) and tRNA bases (Limbach, et al., 1994, which is incorporatedherein by reference), and the compounds7-deaza-7-hydroxymethyl-2′-deoxyadenosine (C⁷-HOMedA) (Rockhill et al.,1997) and 7-deaza-7-hydroxymethyl-2′-deoxyguanosine (C⁷-HOMedG)(McDougall et al., 2001) may also be further modified in the mannerdescribed herein to function as reversible terminators.

In some embodiments described herein, the photocleavable group is asubstituted 2-nitrobenzyl nucleotide, which may be efficientlyphotochemically cleaved, for example, with 365 nm UV light. See U.S.Patent Appl. Publ. 2010/0041041, which is incorporated herein byreference. It is generally understood the wavelengths >300 nm are usedto minimize damage to DNA and proteins (Corrie, 2005) with severalspecific wavelengths other than 365 nm being 340 nm (Kaplan et al.,1978) and 355 nm (Seo, 2005).

In some embodiments, the 3′-OH unblocked reversible terminatorsdescribed herein typically have several advantages, including, forexample, that photocleavage of only a single bond removes both theterminating and fluorophore groups from the nucleobase. This in turn maybe used to more efficiently restore the nucleotide for a subsequent CRTcycle. A second advantage of 3′-OH unblocked reversible terminatorsprovided herein is that many of these compounds show more favorableenzymatic incorporation and, in some embodiments, can be incorporated asreadily as a natural nucleotide with wild-type DNA polymerases.

One challenge for 3′-OH unblocked terminators is creating theappropriate modifications to the base that lead to termination of DNAsynthesis after a single base addition. This is typically importantbecause an unblocked 3′-OH group is the natural substrate forincorporating the next incoming nucleotide. The compounds describedherein address this challenge. For example, in some embodiments, therethe reversible terminators provided herein lead to termination of DNAsynthesis after a single base addition.

In some embodiments, the compounds disclosed herein may be used in CRTto read directly from genomic DNA. Fragmented genomic DNA can behybridized to a high-density oligonucleotide chip containing primingsites that span selected chromosomes. Each priming sequence is separatedby the estimated read-length of the CRT method. Between base additions,a fluorescent imager can simultaneously image the entire high-densitychip, marking significant improvements in speed and sensitivity. Inspecific embodiments, a fluorophore, which is attached to the benzylgroup having an azido substitution on the alpha carbon or itsderivatives described herein, is removed by a specific chemical orenzymatic reaction releasing the benzyl group for the next round of baseaddition. In another specific embodiments, a fluorophore, which isattached to the benzyl group having an amide substitution on the alphacarbon or its derivatives described herein, is removed by a specificenzymatic or chemical reaction releasing the benzyl group for the nextround of base addition. After approximately 500 CRT cycles, the completeand contiguous genome sequence information can then be compared to thereference human genome to determine the extent and type of sequencevariation in an individual's sample. Reversible terminators that exhibithigher incorporation and deprotection efficiencies will typicallyachieve higher cycle efficiencies, and thus longer read-lengths.

CRT Efficiency is defined by the formula: (RL)^(Ceff)=0.5, where RL isthe read-length in bases and Ceff is the overall cycle efficiency. Inother words, a read-length of 7 bases could be achieved with an overallcycle efficiency of 90%, 70 bases could be achieved with a cycleefficiency of 99% and 700 bases with a cycle efficiency of 99.9%. Theefficiency of incorporation of compounds according to the invention mayrange from about 70% to about 100% of the incorporation of the analogousnative nucleoside. Preferably, the efficiency of incorporation willrange from about 85% to about 100%. Photochemical cleavage efficiencieswill preferably range from about 85% to about 100%. Further, terminationof nucleic acid extension will range from about 90% to about 100% uponincorporation of compounds according to the invention. Nucleotide andnucleoside compounds in one embodiment have a cycle efficiency of atleast 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%,99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%.

Another aspect of the present invention is directed towards the use ofpyrosequencing, which is a non-electrophoretic, bioluminescence methodthat measures the release of inorganic pyrophosphate (PPi) byproportionally converting it into visible light by a series of enzymaticreactions (Ronaghi et al., 1998, which is incorporated herein byreference). Unlike other sequencing approaches that use modifiednucleotides to terminate DNA synthesis, the pyrosequencing assaymanipulates DNA polymerase by the single addition of a dNTP in limitingamounts. DNA polymerase then extends the primer upon incorporation ofthe complementary dNTP and pauses. DNA synthesis is reinitiatedfollowing the addition of the next complementary dNTP in the dispensingcycle. The order and intensity of the light peaks are recorded asflowgrams, revealing the underlying DNA sequence. For homopolymerrepeats up to six nucleotides, the number of dNTPs added is directlyproportional to the light signal. Homopolymer repeats greater than sixnucleotide can result in insertion errors, which are the most commonerror type for pyrosequencing. Modified nucleotide analogs of thepresent invention may improve this technology by accurate sequencingthrough homopolymer repeats, particularly those greater than sixnucleotides in length.

Another aspect of the present invention is directed towards the use ofSanger sequencing, for example, as applied to heterozygote detection.Despite much advancement, improvements in the dideoxy-BigDye terminatorsequencing chemistry for accurate heterozygote detection are needed. Itis generally believed that a uniform peak height distribution in theprimary data makes base-calling and heterozygote detection more reliableand accurate. The termination pattern in Sanger sequencing is primarilydue to sequence-dependent bias incorporation by DNA polymerase, whichcan selectively incorporate natural nucleotides over modifiednucleotides (Metzker et al., 1998, which is incorporated herein byreference). These bias incorporation effects are more pronounced withthe dye-terminator chemistry than with the dye-primer chemistry. Thiscan be attributed to effects of the large fluorescent dye structuresattached to the terminating nucleotide, lowering enzyme activity atleast 10-fold to that of the natural substrate. Thus, the reduction ofbias incorporation effects by DNA polymerase towards dye-labeledterminators could lead to improved heterozygote detection. Modifiednucleotide analogs of the present invention may improve this technologyby incorporating as well or better than a natural nucleotide, thuseliminating incorporation bias in Sanger sequencing.

Another aspect of the present invention is directed towards the use ofclonally amplified templates and single DNA molecule templates. Thefront-end of NGS technologies can be partitioned into two camps:clonally amplified templates from single DNA molecules and single DNAmolecule templates. It is well recognized in the art that DNA can beimmobilized to a solid surface by either attaching a primer to saidsurface and hybridizing a target nucleic acid to said primer (U.S. Pat.No. 5,770,367; Harris et al., 2008, which are incorporated herein byreference) or by attaching a target nucleic acid to said surface byclonally amplification and hybridizing a primer to said target nucleicacid (Dressman et al., 2003; Margulies et al., 2005, which areincorporated herein by reference). Either immobilization configurationcan be used in the present invention for then binding a DNA polymeraseto initiate either the CRT method or the pyrosequencing method.

An aspect, the present invention is directed towards the use of singletemplate molecules, that consist of large DNA fragments (i.e., 0.1-0.5megabase). In some embodiments, an adaptor-free strategy called RandomNick Sequencing (RNS) can be employed. It has several advantagesincluding (a) no requirement for PCR or adaptor ligation, (b) redundantsequencing of the same template to improve accuracy, and (c) visiblesequencing reaction sites across the single molecule template providinglocalized de novo assemblies. For example, the PCR process createsmutations in clonally amplified templates that masquerade as sequencevariants. AT-rich and GC-rich target sequences may also showamplification bias in product yield, resulting in theirunderrepresentation in genome alignments and assemblies. Knowing thelocation of sequencing reactions for a given single molecule templatewill simplify the location assignment and organization of complexgenomic and structural regions in the assembly of genomes.

In RNS approach, sugar-nonspecific nucleases such as that isolated fromVibrio vulnificus (vvn) create random single-stranded nicks in dsDNA anddigest both ssDNA and RNA (See Hsia et al., 2005). Vvn binding occurs inthe minor groove of DNA, avoiding sequence-dependent recognition ofnucleobases. This represents an advantage in nicking along a DNAmolecule in a random fashion without sequence-dependent bias. Theupstream strand of the nick becomes a priming site for polymerase tobegin the RNS reaction. For this approach to work in some embodiments,the polymerase must be able to displace the downstream strand whileextending the upstream strand. Several well-known DNA polymerases thatpossess this property include φ29 (See Soengas et al., 1995, which isincorporated herein by reference) and Bst (See Aliotta et al., 1996,which is incorporated herein by reference) polymerases. Vent(exo-) (seeGardner et al., 1999, which is incorporated herein by reference) andTherminator™ polymerases also show strand displacement properties,albeit maybe limited to 50 bases before stalling. Following UV cleavage,hydroxymethyl nucleotides are created which serve as excellent templatebases for subsequent rounds of RNS (FIG. 13). The strand displacementduring RNS creates a bifurcated dsDNA (flap) structure similar to thatcreated with the Invader assay (See Lyamichev et al., 1999). Flapendonucleases (FEN1) are known to cleave these bifurcated structures asshown in FIG. 13, generating a downstream 5′-PO₄ end strand without anucleotide gap (Kaiser et al., 1999). This creates a ligatable substrateto repair the dsDNA molecule for subsequent rounds of RNS.

B. Polymerase Assays

Another aspect of the present invention is directed towards the use ofpolymerase assays. Natural and modified nucleotides were tested forincorporation efficiency using the “polymerase end point assay” (Wu etal., 2007, which is incorporated herein by reference). This assayexamines incorporation efficiency on matched and mismatched templatebases. Incorporation efficiency is measured by determining theconcentration at which the compound incorporates on half theprimer-template complexes (IC₅₀). Titrations of increasing compoundconcentration were performed to generate curves from which the IC₅₀ canbe determined.

The sequence of the template DNA is selected depending on which compoundwill be tested. For example, the first interrogation base after theprimer in the template sequence is the complement base of the compoundwhen measuring incorporation efficiency, and one of three mismatchedbases when measuring mismatch discrimination properties.

To the annealed reaction, a DNA polymerase (e.g., THERMINATOR™ DNApolymerase, 0.25 units per reaction, New England Biolabs), 1× ThermopolBuffer, and a known concentration of either natural or modifiednucleotide are added to each 10 μL reaction and incubated at 75° C. for10 minutes, cooled on ice, and quenched with 10 μL of stop solution (98%formamide: 10 mM Na₂EDTA, pH=8.0, 25 mg/ml Blue Dextran). Stoppedreactions are heated to 75° C. for 30 seconds to denature the DNA, andthen placed on ice. The extension products are analyzed on a 10% LongRanger (Lonza) polyacrylamide gel using an ABI model 377 DNA sequencer.Additional details are provided in Example 1, below.

C. Mismatch Discrimination and Termination

Another aspect of the present invention is directed towards improveddiscrimination against mismatch incorporation, for example, through theuse of the reversible terminators described herein. It has been reportedthat substitution at the α-carbon of the 2-nitrobenzyl group canincrease the rate of the cleavage reaction (Reichmanis et al., 1985;Cameron and Frechet, 1991; Hasan et al., 1997, all three areincorporated herein by reference). Without being bound by theory, theresults presented herein suggest that substitution at the α-carbon ofthe 2-nitrobenzyl group can also affect the termination of DNA synthesisfor 3′-OH unblocked nucleotide triphosphates and improve discriminationagainst mismatch incorporation. Furthermore, and based on the resultsdiscussed in greater detail below, it was found that the stereochemistryof the substitution of α-carbon of the 2-nitrobenzyl group can have asignificant impact on the extent of mismatch discrimination and the rateof the cleavage reaction. Without being bound by theory, at least twofactors were found to typically influence termination of DNA synthesisafter a single incorporation: a) substitution at the α-carbon of the2-nitrobenzyl group, and b) substitution at the 2-position of the benzylring.

D. UV-Cleavage Rates

Another aspect of the present invention is directed towards providingreversible terminators with improved UV-cleavage rates. Cleavage of theterminating substituted 2-nitrobenyl group when analogs are incorporatedinto the primer strand with 365 nm UV light allows for the next cycle ofincorporation to resume. Without being bound by theory, at least twofactors were found typically influence UV-cleavage rates of incorporatednucleotide analogs: a) stereo-chemistry of the α-carbon substitution ofthe 2-nitrobenzyl group, and b) substitution on the benzyl ring.

E. Next-Generation Sequencing (NGS) Technologies

Another aspect of the present invention is directed towards applying thereversible terminators and methods provided herein to next-generationsequencing methods. Sequencing technologies include a number of methodsthat are grouped broadly as (a) template preparation, (b) sequencing andimaging, and (c) data analysis. The unique combination of specificprotocols distinguishes one technology from another and determines thetype of data produced from each platform. These differences in dataoutput present challenges when comparing platforms based on data qualityand cost. Although quality scores and accuracy estimates are provided byeach manufacturer, there is no consensus that a ‘quality base’ from oneplatform is equivalent to that from another platform. The compounds andmethods described herein may be used in combination with and/or appliedto one or more of the template formats described below.

Methods used in preparing templates for NGS reactions include: clonallyamplified templates originating from single DNA molecules, and singleDNA molecule templates. Sequencing methods that use DNA polymerases areclassified as cyclic reversible termination (CRT), single-nucleotideaddition (SNA) and real-time sequencing. Sequencing by ligation (SBL),an approach in which DNA polymerase is replaced by DNA ligase, has alsobeen used in the NGS technologies. See, e.g., Shendure et al., 2005 andValouev et al., 2008, which are incorporated herein by reference.Imaging methods coupled with these sequencing strategies range frommeasuring bioluminescent signals to four-color imaging of singlemolecular events. In some embodiments, such combined methods are furthercombined with suitable information technology systems capable ofhandling the voluminous data produced by NGS platforms, includingaspects related to data storage, tracking and quality control. See Pop &Salzberg, 2008, which is incorporated herein by reference.

a) Template Preparation

In some embodiments, the present invention is directed towards applyingand/or combining the reversible terminators and sequencing methods withone or more templates or template preparation methods. For example, insome embodiments, robust template preparation methods are used. Theseproduce representative, non-biased sources of nucleic acid material fromthe genome under investigation. In some embodiments, the method involvesrandomly breaking genomic DNA into smaller sizes from which eitherfragment templates or mate-pair templates are created. In someembodiments, for example those associated with NGS technologies, thetemplate is attached or immobilized to a solid surface or support. Theimmobilization of spatially separated template sites may be used toallow for thousands to billions of sequencing reactions to be performedsimultaneously.

Clonally Amplified Templates.

In some embodiments, the present invention comprises the use of clonallyamplified templates or clonally amplified template preparation methods.For example, such templates may be used with imaging systems that havenot been designed to detect single fluorescent events. For example, twocommon amplification methods are emulsion PCR (also called emPCR) andsolid-phase amplification. See Dressman et al., 2003 and Fedurco et al.,2006, which are both incorporated herein by reference. In someembodiments, emPCR may be used to prepare sequencing templates in acell-free system, which has the advantage of avoiding the arbitrary lossof genomic sequences—a problem that is typically inherent in bacterialcloning methods. In some embodiments, a library of fragment or mate-pairtargets is created, and adaptors containing universal priming sites areligated to the target ends, allowing complex genomes to be amplifiedwith common PCR primers. For example, after ligation, the DNA isseparated into single strands and captured onto beads under conditionsthat favor one DNA molecule per bead. See Metzker 2010, FIG. 1 a, whichis incorporated herein by reference. For example, after the successfulamplification and enrichment of emPCR beads, millions can be immobilizedin a polyacrylamide gel on a standard microscope slide (used with thePolonator instrument; See, e.g., Shendure et al., 2005, which isincorporated herein by reference), chemically crosslinked to anaminocoated glass surface (used with the Life/APG SOLiD and Polonatorinstruments; see, e.g., Kim et al., 2007, which is incorporated hereinby reference) or deposited into either individual PicoTiterPlate (PTP)wells (used with the Roche/454 instrument; Margulies et al., 2005, whichis incorporated herein by reference) or IonChip well (used with the IonTorrent instrument; Rothberg et al., 2011, which is incorporated hereinby reference) in which the NGS chemistry can be performed. In someembodiments, solid-phase amplification may be used to produce randomlydistributed, clonally amplified clusters from fragment or mate-pairtemplates on a glass slide. See Metzker 2010, FIG. 1 b, which isincorporated herein by reference. In some embodiments, high-densityforward and reverse primers are covalently attached to the slide, andthe ratio of the primers to the template on the support defines thesurface density of the amplified clusters. In some embodiments,solid-phase amplification may be used to produce 100-200 millionspatially separated template clusters (Illumina/Solexa), providing freeends to which a universal sequencing primer can be hybridized toinitiate the NGS reaction. See Bentley et al., 2008, which isincorporated herein by reference.

Single-Molecule Templates.

In some embodiments, the present invention comprises the use ofsingle-molecule templates or single-molecule template preparationmethods. Although clonally amplified methods offer certain advantagesover bacterial cloning, some of the protocols are cumbersome toimplement and require a large amount of genomic DNA material (3-20 μg).The preparation of single-molecule templates is typically morestraightforward and requires less starting material (<1 μg). In someembodiments, these methods do not require PCR, which typically createmutations in clonally amplified templates that masquerade as sequencevariants. AT-rich and GC-rich target sequences may also showamplification bias in product yield, which results in theirunderrepresentation in genome alignments and assemblies. In someembodiments, quantitative applications, such as RNA-seq may be used. SeeWang et al., 2009, which is incorporated herein by reference. Suchapplications typically perform more effectively with non-amplifiedtemplate sources, which do not alter the representational abundance ofmRNA molecules. In some embodiments, and before the NGS reaction iscarried out, single molecule templates are usually immobilized on solidsupports using one of at least three different approaches. In the firstapproach, which may be used in some embodiments, spatially distributedindividual primer molecules are covalently attached to the solid support(See Harris et al., 2008). The template, which may be prepared, forexample, by randomly fragmenting the starting material into small sizes(for example, ˜200-250 bp) and adding common adaptors to the fragmentends, is then hybridized to the immobilized primer. See Metzker 2010,FIG. 1 c, which is incorporated herein by reference. In the secondapproach, which may be used in some embodiments, spatially distributedsingle-molecule templates are covalently attached to the solid support(See Harris et al., 2008) by priming and extending single-stranded,single-molecule templates from immobilized primers. See Metzker 2010,FIG. 1 c, which is incorporated herein by reference. In someembodiments, a common primer is then hybridized to the template. SeeMetzker 2010, FIG. 1 d, which is incorporated by reference. In eitherapproach, DNA polymerase may be used, for example, to bind to theimmobilized primed template configuration to initiate the NGS reaction.In a third approach, which may be used in some embodiments, spatiallydistributed single polymerase molecules are attached to the solidsupport (see Eid et al., 2009, which is incorporated herein byreference), to which a primed template molecule is bound (see Metzker2010, FIG. 1 e, which is incorporated herein by reference). In general,see U.S. Pat. Nos. 7,329,492 and 6,255,083, which are incorporatedherein by reference. Larger DNA molecules (up to tens of thousands ofbase pairs) may be used with this technique, for example, and, unlikethe first two approaches, the third approach can be used with real-timemethods, resulting in potentially longer read lengths.

b) Sequencing and Imaging

There are fundamental differences in sequencing clonally amplified andsingle-molecule templates. Clonal amplification may be used in someembodiments to yield populations of identical templates, each of whichhas undergone the sequencing reaction. Upon imaging, the observed signalis a consensus of the nucleotides or probes added to the identicaltemplates for a given cycle. Typically, this places a greater demand onthe efficiency of the addition process, as incomplete extension of thetemplate ensemble results in lagging-strand dephasing (also called type2 dephasing). The addition of multiple nucleotides or probes can alsooccur in a given cycle, resulting in leading-strand dephasing (alsocalled type 1 dephasing). The concept of dephasing was described byCheeseman (See U.S. Pat. No. 5,302,509, which is incorporated herein byreference). Signal dephasing increases fluorescence noise, causingbase-calling errors and shorter reads (See Erlich et al., 2008). Becausedephasing is not an issue with single-molecule templates, therequirement for cycle efficiency is relaxed. Single molecules, however,are susceptible to multiple nucleotide or probe additions in any givencycle. Here, deletion errors may be observed to occur, in someembodiments, owing to quenching effects between adjacent dye moleculesor no signal will be detected because of the incorporation of darknucleotides or probes. In the following sections, sequencing and imagingstrategies that use both clonally amplified and single-moleculetemplates are discussed. In some aspects of the present inventions, thereversible terminators the method of use provided herein may be appliedand/or used in combination with any one or more of the DNApolymerase-dependent strategies, including, for example, CRT, SNA, andreal-time sequencing. In some embodiments, compounds of the presentinvention and their method of use can be applied to and/or used incombination with the CRT method.

There are several commercially available NGS system that imagingfluorescent signals for single DNA molecules (See Harris et al., 2008;Eid et al., 2009, both of which are incorporated herein by reference).Resolving single molecules on the array can be done it at 100×magnification with a high sensitivity CCD camera, so long as theindividual DNA molecules are separated by a distance that approximatesthe diffraction limit of light (i.e., 250 nm). Variations can occur thatcan depend on magnification and surface flatness, which should beobvious to one of ordinary skill in the art. One technique that iswidely used to detection fluorescent signals from single molecules istotal internal reflection fluorescence (TIRF) microscopy. (See Axelrod,1989, which is incorporated herein by reference). Other techniques thatcan be used in the present invention that are known in the art include,but not limited to, scanning near-field optical microscopy (SNOM; SeeMoyer et al., 1993, which is incorporated herein by reference).

F. Imaging System

FIG. 8 illustrates an embodiment of an imaging system 100 for imagingfluorescent signals derived from clonally amplified template. System 100is configured to image a microfluidic flowcell 50 that has been preparedwith micron beads comprising the DNA of interest.

A range of imaging technologies, such as standard four-color imaging orcolor-blind pulse-multiline excitation, may be used in variousembodiments in combination with the 3′-OH unblocked reversibleterminators. The illustrated embodiment is configured for standardfour-colored imaging.

System 100 comprises an imaging device 10 (e.g., a digital camera,photocell, etc.) configured to capture fluorescent signals derived fromemPCR amplified template beads immobilized in microfluidic flowcell 50.

Lamp 14 (e.g., a xenon lamp) creates a light path 30 betweenmicrofluidic flowcell 50 and imaging device 10. Light from lamp 14travels to filter wheel 16. In the illustrated embodiment, filter wheel16 is motorized and comprises four spectral filters such that four-colorimages may be captured. Filter wheel 16 is configured to switch betweeneach of the four spectral filters at each tile position so that imagingdevice 10 may capture four-color images from the incorporated 3′-OHunblocked reversible terminators.

A portion of the light from lamp 14 travels from filter wheel 16 throughobjective lens 18 to microfluidic flowcell 50. Another portion of thelight from lamp 14 travels from filter wheel 16 to imaging device 10. Inthe illustrated embodiment, light path 30 is directed to imaging device10 using mirror 12. In other embodiments no such mirrors may benecessary, while in still other embodiments, two or more mirrors may berequired.

System 100 also comprises an ultraviolet (UV) light source 20 configuredto provide UV light to flowcell 50. UV light source 20 may be alight-emitting diode (LED) in some embodiments, or may be any othersource of UV light.

G. Minimizing Ozone Contamination

In another aspect, this invention provides sequences methods thatminimize the effects of ozone contamination. Ozone (O₃) is an allotropeof oxygen and has both beneficial and detrimental attributes to life onearth. For example, ozone is created in the stratosphere by high energyradiation from the sun that splits molecular oxygen (O₂) into two atoms,which then combine with different O₂ molecules to form O₃. Thisstratospheric layer protects living organisms on the planet from harmfulultraviolet radiation produced by the sun. At the ground level ortroposphere, however, ozone is considered an air pollutant. Ozone isalso created under smog conditions where sunlight acts on thecombination of oxides of nitrogen and volatile organic compounds thatare produced by industrial facilities, electric utilities, motor vehicleexhaust, gasoline vapors, and chemical solvents (See EPA, 2011). Ozonelevels increase during the hot summer months, and the effects of ozonedamage increase with increasing relative humidity levels. Troposphericozone causes severe damage to crops and forests (See Hewitt et al.,1990), numerous respiratory problems in animals and humans (SeeFairchild et al., 1959; Bhalla, 1994), as well as adverse effects withmany consumer products including automobile tires (See Crabtree andKemp, 1946), dyes found in textile materials (See Salvin and Walker,1955) as well as fluorescent dyes used in molecular biology.

From a chemical perspective, ozone is an electrophilic agent that ismost reactive with electron pairs commonly found in olefinic compounds(i.e., chemicals that contain carbon-carbon double bonds). There hasbeen extensive research dedicated to the chemistry of ozone, which iscalled ozonation. An extensive two volume book series provides acomprehensive review that describes the properties of ozone itself andthe numerous reactions it can undergo with organic substrates. Volume 1of this series is dedicated almost exclusively to the reaction of ozonewith olefinic compounds (See Bailey, 1978; Bailey 1982), for whichVolume 1 and 2 are incorporated by reference.

Dyes and dye intermediates are well known in the literature and with themajority of dye types in use today having been discovered more than acentury ago (Gordon and Gregory, 1983). Dyes can be grouped into classesbased on how they are used or based on their chemical structures(Gordon, 2009). For the latter, dyes have been classified into thegeneral classes of (i) azo, (ii) anthraquinone, (iii) benzodifuranone,(iv) polycyclic aromatic carbonyl, (v) indigoid, (vi) polymethine andrelated dyes (i.e., cyanine), (vii) styryl, (viii) di- and triarylcarbonium and related dyes (i.e., fluorescein, rhodamine and theirsulfonated derivatives), (ix) phthalocyanine, (x) quinophthalone, (xi)sulfur, (xii) nitro and nitroso, and (xiii) miscellaneous (i.e.,coumarin and BODIPY) (Gregory, 2009). Most, if not all, dyes and dyeintermediates have a multiplicity of carbon-carbon double bonds thatmake them sensitive to ozonation. In the mid 1970s, Lofquist andcolleagues taught the general conclusion that most dyes would besusceptible to ozonolysis (See U.S. Pat. No. 3,822,996; U.S. Pat. No.3,859,045; U.S. Pat. No. 3,917,499.

The effect of ozone exposure to dyed fabrics is dye fading (e.g., lossof dyefastness), which was first reported in 1955. Salvin and Walkercoined the term “O-fading”, which in their service test of draperyfabrics revealed that ozone caused significant dye fading when exposedto several blue anthraquinone dyes, (i.e., Eastman Blue GLF, AmacelBlue, and Interchemical Blue B) as well as yellow and red anthraquinonedyes (See Salvin, 1955). Other examples of anthraquinone dyes, such asC.I. Basic Blue 47 (See U.S. Pat. No. 3,822,996) and Disperse Blue 3(See U.S. Pat. No. 3,859,045) have been reported to be susceptible toO-fading. High humidity enhances O-fading (See U.S. Pat. No. 3,917,449;U.S. Pat. No. 4,737,155; U.S. Pat. No. 3,822,996; U.S. Pat. No.4,304,568), and for fabrics, it has been suggested that the moistureprovides the dye sufficient mobility to diffuse to the surface of thematerial where the ozonation reaction occurs (See U.S. Pat. No.4,737,155).

Fluorescent dyes, such as those belonging to the polymethine class, havealso been reported susceptibility to ozonation reactions, which reducetheir fluorescent signal intensities. For example, Cy3 and Cy5 dyes havebeen widely used in microarray technologies for gene expression,genotyping, and resequencing applications (See Gershon, 2004). Fare andcolleagues showed results that Cy5 and its sulfonated derivative AlexaFluor 647 were susceptible to ozone damage at exposure levels of 5 to 10ppb within 10 to 30 sec (See Fare et al., 2003). Fluorescent intensitylevels were also reduced for Cy3 and its sulfonated derivative AlexaFluor 555 at higher ozone levels (>100 ppb). Kadushin and Getts notethat the starting signal can degrade to ˜10% in 1-5 min (See U.S. PatentAppl. Publication 2004/0110196).

There a large number of chemical reagents, which act as antiozonants.Examples include para-phenyldiamine, dihydroquinoline, thiourea (SeeU.S. Pat. No. 4,737,155; U.S. Pat. No. 4,631,066), saturated alkylsubstituted thiourea, alkyl and aryl phosphites (See U.S. Pat. No.3,822,996), ethoxylated aliphatic tertinary amines (See U.S. Pat. No.3,859,045), substituted piperidine thiourea (See U.S. Pat. No.4,304,568), substituted oxadiazine thiones and substituted thiazinethiones (See U.S. Pat. No. 4,304,568), acrylic polymerase, copolymers ofmethacrylate or ethylacrylate (See U.S. Patent Appl. Publication2004/0110196), and polythiourea (See U.S. Pat. No. 3,917,449). For thepresent invention, thiourea may be used in some embodiments, in one ormore solutions to prevent the ozonolysis of fluorescent dyes in thesequencing reaction. WO 2012/037394, which is incorporated herein byreference, provides methods for using thiourea in combination withmethods involving NGS technologies. In some embodiments, the imagingand/or photochemical cleavage steps may be performed in the presence ofthiourea, for example, at the concentrations disclosed in the inventionsummary above.

H. Sample Preparation

Methods to prepare the DNA of interest for NGS analysis include, forexample, clonally-amplified and non-amplified (i.e., single molecule)templates. In some embodiments, emulsion PCR (emPCR) may be used. Asshown in FIG. 9, samples may be prepared as follows. First, genomic DNAis isolated. The DNA is then fragmented into smaller pieces. Then,common adaptors are ligated to the ends of those fragments. Theadaptor-ligated DNA molecules are then separated into single strands andcaptured onto 1 μm size beads under conditions that favor one DNAmolecule per bead. An oil-aqueous emulsion creates individual aqueousdroplets that encapsulate these bead-DNA complexes. PCR amplification isperformed within these droplets to create beads containing 10⁴-10⁶copies of the same template sequence. Following successful amplificationand enrichment, tens of millions to hundreds of millions of emPCR beadsare then chemically immobilized to microfluidic flowcell 50. In someembodiments, flowcell 50 may comprise eight channels and may be made ofglass.

I. System Operation

Once flowcell 50 is prepared with beads, flowcell 50 may be placed inthe sequencing system 100. FIG. 10 illustrates the typical steps in oneCRT cycle. A single DNA molecule is depicted for illustrative purposes,but those skilled in the art would understand that this process isperformed on many DNA molecules.

First, in the incorporation step, 3′-OH reversible terminators areincorporated using DNA polymerase (depicted as a zipper) as discussedabove.

Next, fluorescently-labeled DNA molecules are imaged. Lamp 14 isactivated such that light path 30 is created from flowcell 50 to imagingdevice 10. Imaging device 10 captures images through the each of thefour spectral filters of filter wheel 16. Using filter-wheel 16, eachspectral channel is imaged in a tiled fashion to capture fluorescentsignals within microfluidic flowcell 50. Base calling is then performedfrom processed fluorescent intensities of individual beads (i.e., apurified blue signal may be called an “A” base as the 3′-OH reversibleterminator was labeled with a blue dye). The read length of the CRTmethod is a direct function of the number cycles that are executed (seeMetzker 2010; Metzker, 2005, which are incorporated herein byreference).

Photochemical cleavage may then be performed. Using UV light source 20,UV light is shined upon flowcell 50. The UV light photochemicallycleaves away the terminating group and the fluorescent group. In thismanner, the modified nucleic acid is restored to its native state.

A wash is then supplied, washing away the terminating group andfluorescent groups. The incorporation, imaging, cleaving and washingsteps may be performed for as many CRT cycles as desired. FIG. 11illustrates four-color tile images from three cycles and subsequentbase-calling from individual beads.

IV. Definitions

When used in the context of a chemical group, “hydrogen” means —H;“hydroxy” means —OH; “oxo” means ═O; “halo” means independently —F, —Cl,—Br or —I; “amino” means —NH₂; “hydroxyamino” means —NHOH; “nitro” means—NO₂; imino means ═NH; “cyano” means —CN; “isocyanate” means —N═C═O;“azido” means —N₃; in a monovalent context “phosphate” means —OP(O)(OH)₂or a deprotonated form thereof; in a divalent context “phosphate” means—OP(O)(OH)O— or a deprotonated form thereof; “mercapto” means —SH; and“thio” means ═S; “sulfonyl” means —S(O)₂—; and “sulfinyl” means —S(O)—.

In the context of chemical formulas, the symbol “—” means a single bond,“═” means a double bond, and “≡” means triple bond. The symbol “----”represents an optional bond, which if present is either single ordouble. The symbol “

” represents a single bond or a double bond. Thus, for example, thestructure

includes the structures

and

As will be understood by a person of skill in the art, no one such ringatom forms part of more than one double bond. The symbol “

”, when drawn perpendicularly across a bond indicates a point ofattachment of the group. It is noted that the point of attachment istypically only identified in this manner for larger groups in order toassist the reader in rapidly and unambiguously identifying a point ofattachment. The symbol “

” means a single bond where the group attached to the thick end of thewedge is “out of the page.” The symbol “

” means a single bond where the group attached to the thick end of thewedge is “into the page”. The symbol “

” means a single bond where the conformation (e.g., either R or S) orthe geometry is undefined (e.g., either E or Z).

Any undefined valency on an atom of a structure shown in thisapplication implicitly represents a hydrogen atom bonded to the atom.When a group “R” is depicted as a “floating group” on a ring system, forexample, in the formula:

then R may replace any hydrogen atom attached to any of the ring atoms,including a depicted, implied, or expressly defined hydrogen, so long asa stable structure is formed. When a group “R” is depicted as a“floating group” on a fused ring system, as for example in the formula:

then R may replace any hydrogen attached to any of the ring atoms ofeither of the fused rings unless specified otherwise. Replaceablehydrogens include depicted hydrogens (e.g., the hydrogen attached to thenitrogen in the formula above), implied hydrogens (e.g., a hydrogen ofthe formula above that is not shown but understood to be present),expressly defined hydrogens, and optional hydrogens whose presencedepends on the identity of a ring atom (e.g., a hydrogen attached togroup X, when X equals —CH—), so long as a stable structure is formed.In the example depicted, R may reside on either the 5-membered or the6-membered ring of the fused ring system. In the formula above, thesubscript letter “y” immediately following the group “R” enclosed inparentheses, represents a numeric variable. Unless specified otherwise,this variable can be 0, 1, 2, or any integer greater than 2, onlylimited by the maximum number of replaceable hydrogen atoms of the ringor ring system.

For the groups and classes below, the following parenthetical subscriptsfurther define the group/class as follows: “(Cn)” defines the exactnumber (n) of carbon atoms in the group/class. “(C≦n)” defines themaximum number (n) of carbon atoms that can be in the group/class, withthe minimum number as small as possible for the group in question, e.g.,it is understood that the minimum number of carbon atoms in the group“alkenyl_((C≦8))” or the class “alkene_((C≦8))” is two. For example,“alkoxy_((C≦10))” designates those alkoxy groups having from 1 to 10carbon atoms (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or any rangederivable therein (e.g., 3 to 10 carbon atoms). (Cn-n′) defines both theminimum (n) and maximum number (n′) of carbon atoms in the group.Similarly, “alkyl_((C2-10))” designates those alkyl groups having from 2to 10 carbon atoms (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10, or any rangederivable therein (e.g., 3 to 10 carbon atoms)).

The term “saturated” as used herein means the compound or group somodified has no carbon-carbon double and no carbon-carbon triple bonds,except as noted below. The term does not preclude carbon-heteroatommultiple bonds, for example a carbon oxygen double bond or a carbonnitrogen double bond. Moreover, it does not preclude a carbon-carbondouble bond that may occur as part of keto-enol tautomerism orimine/enamine tautomerism.

The term “aliphatic” when used without the “substituted” modifiersignifies that the compound/group so modified is an acyclic or cyclic,but non-aromatic hydrocarbon compound or group. In aliphaticcompounds/groups, the carbon atoms can be joined together in straightchains, branched chains, or non-aromatic rings (alicyclic). Aliphaticcompounds/groups can be saturated, that is joined by single bonds(alkanes/alkyl), or unsaturated, with one or more double bonds(alkenes/alkenyl) or with one or more triple bonds (alkynes/alkynyl).Where the term “aliphatic” is used without the “substituted” modifier,then only carbon and hydrogen atoms are present. When the term is usedwith the “substituted” modifier one or more hydrogen atom has beenindependently replaced by —OH, —F, —Cl, —Br, —I, —NH₂, —NO₂, —CO₂H,—CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃, —NHCH₂CH₃,—N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂.

The term “alkyl” when used without the “substituted” modifier refers toa monovalent saturated aliphatic group with a carbon atom as the pointof attachment, a linear or branched, cyclo, cyclic or acyclic structure,and no atoms other than carbon and hydrogen. Thus, as used hereincycloalkyl is a subset of alkyl. The groups —CH₃ (Me), —CH₂CH₃ (Et),—CH₂CH₂CH₃ (n-Pr or propyl), —CH(CH₃)₂ (i-Pr, ^(i)Pr or isopropyl),—CH(CH₂)₂ (cyclopropyl), —CH₂CH₂CH₂CH₃ (n-Bu), —CH(CH₃)CH₂CH₃(sec-butyl), —CH₂CH(CH₃)₂ (isobutyl), —C(CH₃)₃ (tert-butyl, t-butyl,t-Bu or ^(t)Bu), —CH₂C(CH₃)₃ (neo-pentyl), cyclobutyl, cyclopentyl,cyclohexyl, and cyclohexylmethyl are non-limiting examples of alkylgroups. The term “alkanediyl” when used without the “substituted”modifier refers to a divalent saturated aliphatic group, with one or twosaturated carbon atom(s) as the point(s) of attachment, a linear orbranched, cyclo, cyclic or acyclic structure, no carbon-carbon double ortriple bonds, and no atoms other than carbon and hydrogen. The groups,—CH₂—(methylene), —CH₂CH₂—, —CH₂C(CH₃)₂CH₂—, —CH₂CH₂CH₂—, and

are non-limiting examples of alkanediyl groups. The term “alkylidene”when used without the “substituted” modifier refers to the divalentgroup ═CRR′ in which R and R′ are independently hydrogen, alkyl, or Rand R′ are taken together to represent an alkanediyl having at least twocarbon atoms. Non-limiting examples of alkylidene groups include: ═CH₂,═CH(CH₂CH₃), and ═C(CH₃)₂. When any of these terms is used with the“substituted” modifier one or more hydrogen atom has been independentlyreplaced by —OH, —F, —Cl, —Br, —I, —NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH,—OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃, —NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂,—OC(O)CH₃, or —S(O)₂NH₂. The following groups are non-limiting examplesof substituted alkyl groups: —CH₂OH, —CH₂Cl, —CF₃, —CH₂CN, —CH₂C(O)OH,—CH₂C(O)OCH₃, —CH₂C(O)NH₂, —CH₂C(O)CH₃, —CH₂OCH₃, —CH₂OC(O)CH₃, —CH₂NH₂,—CH₂N(CH₃)₂, and —CH₂CH₂Cl. The term “haloalkyl” is a subset ofsubstituted alkyl, in which one or more hydrogen atoms has beensubstituted with a halo group and no other atoms aside from carbon,hydrogen and halogen are present. The group, —CH₂Cl is a non-limitingexample of a haloalkyl. An “alkane” refers to the compound H—R, whereinR is alkyl. The term “fluoroalkyl” is a subset of substituted alkyl, inwhich one or more hydrogen has been substituted with a fluoro group andno other atoms aside from carbon, hydrogen and fluorine are present. Thegroups, —CH₂F, —CF₃, and —CH₂CF₃ are non-limiting examples offluoroalkyl groups. An “alkane” refers to the compound H—R, wherein R isalkyl.

The term “alkenyl” when used without the “substituted” modifier refersto an monovalent unsaturated aliphatic group with a carbon atom as thepoint of attachment, a linear or branched, cyclo, cyclic or acyclicstructure, at least one nonaromatic carbon-carbon double bond, nocarbon-carbon triple bonds, and no atoms other than carbon and hydrogen.Non-limiting examples of alkenyl groups include: —CH═CH₂ (vinyl),—CH═CHCH₃, —CH═CHCH₂CH₃, —CH₂CH═CH₂ (allyl), —CH₂CH═CHCH₃, and—CH═CH—C₆H₅. The term “alkenediyl” when used without the “substituted”modifier refers to a divalent unsaturated aliphatic group, with twocarbon atoms as points of attachment, a linear or branched, cyclo,cyclic or acyclic structure, at least one nonaromatic carbon-carbondouble bond, no carbon-carbon triple bonds, and no atoms other thancarbon and hydrogen. The groups, —CH═CH—, —CH═C(CH₃)CH₂—, —CH═CHCH₂—,and

are non-limiting examples of alkenediyl groups.

When these terms are used with the “substituted” modifier one or morehydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I,—NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃,—NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂. The groups,—CH═CHF, —CH═CHCl and —CH═CHBr, are non-limiting examples of substitutedalkenyl groups. An “alkene” refers to the compound H—R, wherein R isalkenyl.

The term “alkynyl” when used without the “substituted” modifier refersto an monovalent unsaturated aliphatic group with a carbon atom as thepoint of attachment, a linear or branched, cyclo, cyclic or acyclicstructure, at least one carbon-carbon triple bond, and no atoms otherthan carbon and hydrogen. As used herein, the term alkynyl does notpreclude the presence of one or more non-aromatic carbon-carbon doublebonds. The groups, —C≡CH, —C≡CCH₃, and —CH₂C≡CCH₃, are non-limitingexamples of alkynyl groups. When alkynyl is used with the “substituted”modifier one or more hydrogen atom has been independently replaced by—OH, —F, —Cl, —Br, —I, —NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃,—OCH₂CH₃, —C(O)CH₃, —NHCH₃, —NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or—S(O)₂NH₂. An “alkyne” refers to the compound H—R, wherein R is alkynyl.

The term “aryl” when used without the “substituted” modifier refers to amonovalent unsaturated aromatic group with an aromatic carbon atom asthe point of attachment, said carbon atom forming part of a one or moresix-membered aromatic ring structure, wherein the ring atoms are allcarbon, and wherein the group consists of no atoms other than carbon andhydrogen. If more than one ring is present, the rings may be fused orunfused. As used herein, the term does not preclude the presence of oneor more alkyl group (carbon number limitation permitting) attached tothe first aromatic ring or any additional aromatic ring present.Non-limiting examples of aryl groups include phenyl (Ph), methylphenyl,(dimethyl)phenyl, —C₆H₄CH₂CH₃ (ethylphenyl), naphthyl, and themonovalent group derived from biphenyl. The term “arenediyl” when usedwithout the “substituted” modifier refers to a divalent aromatic groupwith two aromatic carbon atoms as points of attachment, said carbonatoms forming part of one or more six-membered aromatic ringstructure(s) wherein the ring atoms are all carbon, and wherein themonovalent group consists of no atoms other than carbon and hydrogen. Asused herein, the term does not preclude the presence of one or morealkyl group (carbon number limitation permitting) attached to the firstaromatic ring or any additional aromatic ring present. If more than onering is present, the rings may be fused or unfused. Non-limitingexamples of arenediyl groups include:

and

When these terms are used with the “substituted” modifier one or morehydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I,—NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃,—NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂. An “arene”refers to the compound H—R, wherein R is aryl.

The term “aralkyl” when used without the “substituted” modifier refersto the monovalent group -alkanediyl-aryl, in which the terms alkanediyland aryl are each used in a manner consistent with the definitionsprovided above. Non-limiting examples of aralkyls are: phenylmethyl(benzyl, Bn) and 2-phenyl-ethyl. When the term is used with the“substituted” modifier one or more hydrogen atom from the alkanediyland/or the aryl has been independently replaced by —OH, —F, —Cl, —Br,—I, —NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃,—NHCH₃, —NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂.Non-limiting examples of substituted aralkyls are:(3-chlorophenyl)-methyl, and 2-chloro-2-phenyl-eth-1-yl.

The term “heteroaryl” when used without the “substituted” modifierrefers to a monovalent aromatic group with an aromatic carbon atom ornitrogen atom as the point of attachment, said carbon atom or nitrogenatom forming part of one or more aromatic ring structures wherein atleast one of the ring atoms is nitrogen, oxygen or sulfur, and whereinthe heteroaryl group consists of no atoms other than carbon, hydrogen,aromatic nitrogen, aromatic oxygen and aromatic sulfur. As used herein,the term does not preclude the presence of one or more alkyl, aryl,and/or aralkyl groups (carbon number limitation permitting) attached tothe aromatic ring or aromatic ring system. If more than one ring ispresent, the rings may be fused or unfused. Non-limiting examples ofheteroaryl groups include furanyl, imidazolyl, indolyl, indazolyl (Im),isoxazolyl, methylpyridinyl, oxazolyl, phenylpyridinyl, pyridinyl,pyrrolyl, pyrimidinyl, pyrazinyl, quinolyl, quinazolyl, quinoxalinyl,triazinyl, tetrazolyl, thiazolyl, thienyl, and triazolyl. The term“N-heteroaryl” refers to a heteroaryl group with a nitrogen atom as thepoint of attachment. The term “heteroarenediyl” when used without the“substituted” modifier refers to an divalent aromatic group, with twoaromatic carbon atoms, two aromatic nitrogen atoms, or one aromaticcarbon atom and one aromatic nitrogen atom as the two points ofattachment, said atoms forming part of one or more aromatic ringstructure(s) wherein at least one of the ring atoms is nitrogen, oxygenor sulfur, and wherein the divalent group consists of no atoms otherthan carbon, hydrogen, aromatic nitrogen, aromatic oxygen and aromaticsulfur. As used herein, the term does not preclude the presence of oneor more alkyl, aryl, and/or aralkyl groups (carbon number limitationpermitting) attached to the aromatic ring or aromatic ring system. Ifmore than one ring is present, the rings may be fused or unfused.Non-limiting examples of heteroarenediyl groups include:

and

When these terms are used with the “substituted” modifier one or morehydrogen atom has been independently replaced by —OH, —F, —Cl, —Br, —I,—NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃,—NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂.

The term “heterocycloalkyl” when used without the “substituted” modifierrefers to a monovalent non-aromatic group with a carbon atom or nitrogenatom as the point of attachment, said carbon atom or nitrogen atomforming part of one or more non-aromatic ring structures wherein atleast one of the ring atoms is nitrogen, oxygen or sulfur, and whereinthe heterocycloalkyl group consists of no atoms other than carbon,hydrogen, nitrogen, oxygen and sulfur. As used herein, the term does notpreclude the presence of one or more alkyl groups (carbon numberlimitation permitting) attached to the ring or ring system. As usedherein, the term does not preclude the presence of one or more doublebonds in the ring or ring system, provided that the resulting groupsremains non-aromatic. If more than one ring is present, the rings may befused or unfused. Non-limiting examples of heterocycloalkyl groupsinclude aziridinyl, azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl,morpholinyl, thiomorpholinyl, tetrahydrofuranyl, tetrahydrothiofuranyl,tetrahydropyranyl, pyranyl, oxiranyl, and oxetanyl. The term“N-heterocycloalkyl” refers to a heterocycloalkyl group with a nitrogenatom as the point of attachment. When the term “heterocycloalkyl” usedwith the “substituted” modifier one or more hydrogen atom has beenindependently replaced by —OH, —F, —Cl, —Br, —I, —NH₂, —NO₂, —CO₂H,—CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃, —NHCH₂CH₃,—N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, —S(O)₂NH₂, or —C(O)OC(CH₃)₃(tert-butyloxycarbonyl, BOC).

The term “acyl” when used without the “substituted” modifier refers tothe group —C(O)R, in which R is a hydrogen, alkyl, aryl, aralkyl orheteroaryl, as those terms are defined above. The groups, —CHO, —C(O)CH₃(acetyl, Ac), —C(O)CH₂CH₃, —C(O)CH₂CH₂CH₃, —C(O)CH(CH₃)₂, —C(O)CH(CH₂)₂,—C(O)C₆H₅, —C(O)C₆H₄CH₃, —C(O)CH₂C₆H₅, —C(O)(imidazolyl) arenon-limiting examples of acyl groups. A “thioacyl” is defined in ananalogous manner, except that the oxygen atom of the group —C(O)R hasbeen replaced with a sulfur atom, —C(S)R. When either of these terms areused with the “substituted” modifier one or more hydrogen atom(including a hydrogen atom directly attached the carbonyl orthiocarbonyl group, if any) has been independently replaced by —OH, —F,—Cl, —Br, —I, —NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃,—C(O)CH₃, —NHCH₃, —NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or—S(O)₂NH₂. The groups, —C(O)CH₂CF₃, —CO₂H (carboxyl), —CO₂CH₃(methylcarboxyl), —CO₂CH₂CH₃, —C(O)NH₂ (carbamoyl), and —CON(CH₃)₂, arenon-limiting examples of substituted acyl groups.

The term “alkoxy” when used without the “substituted” modifier refers tothe group —OR, in which R is an alkyl, as that term is defined above.Non-limiting examples of alkoxy groups include: —OCH₃ (methoxy),—OCH₂CH₃ (ethoxy), —OCH₂CH₂CH₃, —OCH(CH₃)₂ (isopropoxy), —O(CH₃)₃(tert-butoxy), —OCH(CH₂)₂, —O— cyclopentyl, and —O-cyclohexyl. The terms“alkenyloxy”, “alkynyloxy”, “aryloxy”, “aralkoxy”, “heteroaryloxy”,“heterocycloalkoxy”, and “acyloxy”, when used without the “substituted”modifier, refers to groups, defined as —OR, in which R is alkenyl,alkynyl, aryl, aralkyl, heteroaryl, heterocycloalkyl, and acyl,respectively. The term “alkoxydiyl” refers to the divalent group—O-alkanediyl-, —O-alkanediyl-O—, or -alkanediyl-O-alkanediyl-. The term“alkylthio” and “acylthio” when used without the “substituted” modifierrefers to the group —SR, in which R is an alkyl and acyl, respectively.When any of these terms is used with the “substituted” modifier one ormore hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br,—I, —NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃,—NHCH₃, —NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂. The term“alcohol” corresponds to an alkane, as defined above, wherein at leastone of the hydrogen atoms has been replaced with a hydroxy group.

The term “alkylamino” when used without the “substituted” modifierrefers to the group —NHR, in which R is an alkyl, as that term isdefined above. Non-limiting examples of alkylamino groups include:—NHCH₃ and —NHCH₂CH₃. The term “dialkylamino” when used without the“substituted” modifier refers to the group —NRR′, in which R and R′ canbe the same or different alkyl groups, or R and R′ can be taken togetherto represent an alkanediyl. Non-limiting examples of dialkylamino groupsinclude: —N(CH₃)₂, —N(CH₃)(CH₂CH₃), and N-pyrrolidinyl. The terms“alkoxyamino”, “alkenylamino”, “alkynylamino”, “arylamino”,“aralkylamino”, “heteroarylamino”, “heterocycloalkylamino” and“alkylsulfonylamino” when used without the “substituted” modifier,refers to groups, defined as —NHR, in which R is alkoxy, alkenyl,alkynyl, aryl, aralkyl, heteroaryl, heterocycloalkyl, and alkylsulfonyl,respectively. A non-limiting example of an arylamino group is —NHC₆H₅.The term “amido” (acylamino), when used without the “substituted”modifier, refers to the group —NHR, in which R is acyl, as that term isdefined above. A non-limiting example of an amido group is —NHC(O)CH₃.The term “alkylimino” when used without the “substituted” modifierrefers to the divalent group ═NR, in which R is an alkyl, as that termis defined above. The term “alkylaminodiyl” refers to the divalent group—NH— alkanediyl-, —NH— alkanediyl-NH—, or -alkanediyl-NH-alkanediyl-.When any of these terms is used with the “substituted” modifier one ormore hydrogen atom has been independently replaced by —OH, —F, —Cl, —Br,—I, —NH₂, —NO₂, —CO₂H, —CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃,—NHCH₃, —NHCH₂CH₃, —N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂. Thegroups —NHC(O)OCH₃ and —NHC(O)NHCH₃ are non-limiting examples ofsubstituted amido groups.

The term “alkylphosphate” when used without the “substituted” modifierrefers to the group —OP(O)(OH)(OR), in which R is an alkyl, as that termis defined above. Non-limiting examples of alkylphosphate groupsinclude: —OP(O)(OH)(OMe) and —OP(O)(OH)(OEt). The term“dialkylphosphate” when used without the “substituted” modifier refersto the group —OP(O)(OR)(OR′), in which R and R′ can be the same ordifferent alkyl groups, or R and R′ can be taken together to representan alkanediyl. Non-limiting examples of dialkylphosphate groups include:—OP(O)(OMe)₂, —OP(O)(OEt)(OMe) and —OP(O)(OEt)₂. When any of these termsis used with the “substituted” modifier one or more hydrogen atom hasbeen independently replaced by —OH, —F, —Cl, —Br, —I, —NH₂, —NO₂, —CO₂H,—CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃, —NHCH₂CH₃,—N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂.

The terms “alkylsulfonyl” and “alkylsulfinyl” when used without the“substituted” modifier refers to the groups —S(O)₂R and —S(O)R,respectively, in which R is an alkyl, as that term is defined above. Theterms “alkenylsulfonyl”, “alkynylsulfonyl”, “arylsulfonyl”,“aralkylsulfonyl”, “heteroarylsulfonyl”, and “heterocycloalkylsulfonyl”are defined in an analogous manner. When any of these terms is used withthe “substituted” modifier one or more hydrogen atom has beenindependently replaced by —OH, —F, —Cl, —Br, —I, —NH₂, —NO₂, —CO₂H,—CO₂CH₃, —CN, —SH, —OCH₃, —OCH₂CH₃, —C(O)CH₃, —NHCH₃, —NHCH₂CH₃,—N(CH₃)₂, —C(O)NH₂, —OC(O)CH₃, or —S(O)₂NH₂.

As used herein, a “chiral auxiliary” refers to a removable chiral groupthat is capable of influencing the stereoselectivity of a reaction.Persons of skill in the art are familiar with such compounds, and manyare commercially available.

The use of the word “a” or “an,” when used in conjunction with the term“comprising” in the claims and/or the specification may mean “one,” butit is also consistent with the meaning of “one or more,” “at least one,”and “one or more than one.”

Throughout this application, the term “about” is used to indicate that avalue includes the inherent variation of error for the device, themethod being employed to determine the value, or the variation thatexists among the study subjects.

The terms “comprise,” “have” and “include” are open-ended linking verbs.Any forms or tenses of one or more of these verbs, such as “comprises,”“comprising,” “has,” “having,” “includes” and “including,” are alsoopen-ended. For example, any method that “comprises,” “has” or“includes” one or more steps is not limited to possessing only those oneor more steps and also covers other unlisted steps.

The term “effective,” as that term is used in the specification and/orclaims, means adequate to accomplish a desired, expected, or intendedresult. “Effective amount,” “Therapeutically effective amount” or“pharmaceutically effective amount” when used in the context of treatinga patient or subject with a compound means that amount of the compoundwhich, when administered to a subject or patient for treating a disease,is sufficient to effect such treatment for the disease.

The term “hydrate” when used as a modifier to a compound means that thecompound has less than one (e.g., hemihydrate), one (e.g., monohydrate),or more than one (e.g., dihydrate) water molecules associated with eachcompound molecule, such as in solid forms of the compound.

As used herein, the term “IC₅₀” refers to an inhibitory dose which is50% of the maximum response obtained. This quantitative measureindicates how much of a particular drug or other substance (inhibitor)is needed to inhibit a given biological, biochemical or chemical process(or component of a process, i.e. an enzyme, cell, cell receptor ormicroorganism) by half

An “isomer” of a first compound is a separate compound in which eachmolecule contains the same constituent atoms as the first compound, butwhere the configuration of those atoms in three dimensions differs.

As used herein, the term “patient” or “subject” refers to a livingmammalian organism, such as a human, monkey, cow, sheep, goat, dog, cat,mouse, rat, guinea pig, or transgenic species thereof. In certainembodiments, the patient or subject is a primate. Non-limiting examplesof human subjects are adults, juveniles, infants and fetuses.

As generally used herein “pharmaceutically acceptable” refers to thosecompounds, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues, organs, and/or bodily fluids of human beings andanimals without excessive toxicity, irritation, allergic response, orother problems or complications commensurate with a reasonablebenefit/risk ratio.

“Pharmaceutically acceptable salts” means salts of compounds of thepresent invention which are pharmaceutically acceptable, as definedabove, and which possess the desired pharmacological activity. Suchsalts include acid addition salts formed with inorganic acids such ashydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid,phosphoric acid, and the like; or with organic acids such as1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid,2-naphthalenesulfonic acid, 3-phenylpropionic acid,4,4′-methylenebis(3-hydroxy-2-ene-1-carboxylic acid),4-methylbicyclo[2.2.2]oct-2-ene-1-carboxylic acid, acetic acid,aliphatic mono- and dicarboxylic acids, aliphatic sulfuric acids,aromatic sulfuric acids, benzenesulfonic acid, benzoic acid,camphorsulfonic acid, carbonic acid, cinnamic acid, citric acid,cyclopentanepropionic acid, ethanesulfonic acid, fumaric acid,glucoheptonic acid, gluconic acid, glutamic acid, glycolic acid,heptanoic acid, hexanoic acid, hydroxynaphthoic acid, lactic acid,laurylsulfuric acid, maleic acid, malic acid, malonic acid, mandelicacid, methanesulfonic acid, muconic acid, o-(4-hydroxybenzoyl)benzoicacid, oxalic acid, p-chlorobenzenesulfonic acid, phenyl-substitutedalkanoic acids, propionic acid, p-toluenesulfonic acid, pyruvic acid,salicylic acid, stearic acid, succinic acid, tartaric acid,tertiarybutylacetic acid, trimethylacetic acid, and the like.Pharmaceutically acceptable salts also include base addition salts whichmay be formed when acidic protons present are capable of reacting withinorganic or organic bases. Acceptable inorganic bases include sodiumhydroxide, sodium carbonate, potassium hydroxide, aluminum hydroxide andcalcium hydroxide. Acceptable organic bases include ethanolamine,diethanolamine, triethanolamine, tromethamine, N-methylglucamine and thelike. It should be recognized that the particular anion or cationforming a part of any salt of this invention is not critical, so long asthe salt, as a whole, is pharmacologically acceptable. Additionalexamples of pharmaceutically acceptable salts and their methods ofpreparation and use are presented in Handbook of Pharmaceutical Salts:Properties, and Use (P. H. Stahl & C. G. Wermuth eds., Verlag HelveticaChimica Acta, 2002).

The term “pharmaceutically acceptable carrier,” as used herein means apharmaceutically-acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, solvent or encapsulatingmaterial, involved in carrying or transporting a chemical agent.

“Prevention” or “preventing” includes: (1) inhibiting the onset of adisease in a subject or patient which may be at risk and/or predisposedto the disease but does not yet experience or display any or all of thepathology or symptomatology of the disease, and/or (2) slowing the onsetof the pathology or symptomatology of a disease in a subject or patientwhich may be at risk and/or predisposed to the disease but does not yetexperience or display any or all of the pathology or symptomatology ofthe disease.

A “stereoisomer” or “optical isomer” is an isomer of a given compound inwhich the same atoms are bonded to the same other atoms, but where theconfiguration of those atoms in three dimensions differs. “Enantiomers”are stereoisomers of a given compound that are mirror images of eachother, like left and right hands. “Diastereomers” are stereoisomers of agiven compound that are not enantiomers. Chiral molecules contain achiral center, also referred to as a stereocenter or stereogenic center,which is any point, though not necessarily an atom, in a moleculebearing groups such that an interchanging of any two groups leads to astereoisomer. In organic compounds, the chiral center is typically acarbon, phosphorus or sulfur atom, though it is also possible for otheratoms to be stereocenters in organic and inorganic compounds. A moleculecan have multiple stereocenters, giving it many stereoisomers. Incompounds whose stereoisomerism is due to tetrahedral stereogeniccenters (e.g., tetrahedral carbon), the total number of hypotheticallypossible stereoisomers will not exceed 2n, where n is the number oftetrahedral stereocenters. Molecules with symmetry frequently have fewerthan the maximum possible number of stereoisomers. A 50:50 mixture ofenantiomers is referred to as a racemic mixture. Alternatively, amixture of enantiomers can be enantiomerically enriched so that oneenantiomer is present in an amount greater than 50%. Typically,enantiomers and/or diasteromers can be resolved or separated usingtechniques known in the art. It is contemplated that that for anystereocenter or axis of chirality for which stereochemistry has not beendefined, that stereocenter or axis of chirality can be present in its Rform, S form, or as a mixture of the R and S forms, including racemicand non-racemic mixtures. As used herein, the phrase “substantially freefrom other stereoisomers” means that the composition contains ≦15%, morepreferably ≦10%, even more preferably ≦5%, or most preferably ≦1% ofanother stereoisomer(s).

“Treatment” or “treating” includes (1) inhibiting a disease in a subjector patient experiencing or displaying the pathology or symptomatology ofthe disease (e.g., arresting further development of the pathology and/orsymptomatology), (2) ameliorating a disease in a subject or patient thatis experiencing or displaying the pathology or symptomatology of thedisease (e.g., reversing the pathology and/or symptomatology), and/or(3) effecting any measurable decrease in a disease in a subject orpatient that is experiencing or displaying the pathology orsymptomatology of the disease.

The terms “nucleotide base”, “nucleobase” or simply “base”, as usedherein, refers to a substituted or unsubstituted nitrogen-containingparent heteroaromatic ring of a type that is commonly found in nucleicacids, as well as natural, substituted, modified, or engineered variantsor analogs of the same. In a typical embodiment, the nucleobase iscapable of forming Watson-Crick and/or Hoogsteen hydrogen bonds with anappropriately complementary nucleobase. Exemplary nucleobases include,but are not limited to,

-   -   purines such as 2-aminopurine, 2,6-diaminopurine, adenine (A),        ethenoadenine, N⁶-Δ²-isopentenyladenine (6iA),        N⁶-Δ²-isopentenyl-2-methylthioadenine (2ms6iA),        N⁶-methyladenine, guanine (G), isoguanine, N²-dimethylguanine        (dmG), 7-methylguanine (7mG), 2-thiopyrimidine, 6-thioguanine        (6sG), hypoxanthine and O⁶-methylguanine;    -   7-deaza-purines such as 7-deazaadenine (7-deaza-A),        7-deazaguanine (7-deaza-G), 7-deaza-7-hydroxymethyladenine,        7-deaza-7-aminomethyladenine and 7-deaza-7-hydroxymethylguanine;    -   pyrimidines such as cytosine (C), 5-propynylcytosine,        isocytosine, 5-hydroxylmethylcytosine (HOMeC),        5-aminomethyl-cytosine, thymine (T), 4-thiothymine (4sT),        5,6-dihydrothymine, O⁴-methylthymine, uracil (U), 4-thiouracil        (4sU), 5-hydroxylmethyluracil (HOMeU), 5-aminomethyl-uracil, and        5,6-dihydrouracil (dihydrouracil; D);    -   indoles such as nitroindole and 4-methylindole; pyrroles such as        nitropyrrole; nebularine; base (Y); etc.        Additional exemplary nucleobases can be found in Lehninger,        2005, which is incorporated by reference, and the references        cited therein.

The term “nucleoside” as used herein, refers to a glycosylamineconsisting of a nucleobase bound to a five-carbon sugar, typically aribose or a deoxyribose. Examples of these include, but are not limitedto, cytidine, 2′-deoxycytidine, 5-hydroxylmethylcytidine,2′-deoxy-5-hydroxylmethylcytidine, 5-aminomethylcytidine,2′-deoxy-5-aminomethylcytidine, uridine, 2′-deoxyuridine,5-hydroxylmethyluridine, 2′-deoxy-5-hydroxylmethyluridine,5-aminomethyluridine, 2′-deoxy-5-aminomethyluridine, adenosine,2′-deoxyadenosine, 7-deaza-7-hydroxymethyladenosine,2′-deoxy-7-deaza-7-hydroxymethyladenosine,7-deaza-7-aminomethyladenosine, 2′-deoxy-7-deaza-7-aminomethyladenosine,guanosine, 2′-deoxyguanosine, 7-deaza-7-hydroxymethyl guanosine,2′-deoxy-7-deaza-7-hydroxymethyl, 7-deaza-7-aminomethyl guanosine,2′-deoxy-7-deaza-7-aminomethyl guanosine, thymidine, and2′-deoxythymidine.

A “nucleotide” is composed of a nucleoside with one, two, three or morephosphate groups bound in a chain to the 5-carbon sugar of thenucleoside.

The term “dephasing” is a pheonmenon that occurs with step-wise additionmethods, including but not limited to CRT, SNA, and SBL methods, whengrowing primers move out of synchronicity for any given cycle. Laggingstrand or type 2 dephasing (for example, n−1 from the expected cycle)result from incomplete extension, and leading strand or type 1 dephasing(for example, n+1) result from the addition of multiple nucleotides orprobes in a population of identical templates.

The term “dark nucleotide” or “dark probe” refers to a nucleotide orprobe that does not contain a fluorescent label. It can be generatedfrom its cleavage and carry-over from the previous cycle or behydrolyzed in situ from its dye-labeled counterpart in the currentcycle.

Unless specified otherwise, a “linker” refers to one or more divalentgroups (linking members) that function as a covalently-bonded molecularbridge between two other groups. A linker may contain one or morelinking members and one or more types of linking members. Exemplarylinking members include: —C(O)NH—, —C(O)O—, —NH—, —S—, —S(O)_(n)— wheren is 0, 1 or 2, —O—, —OP(O)(OH)O—, —OP(O)(O⁻)O—, alkanediyl, alkenediyl,alkynediyl, arenediyl, heteroarenediyl, or combinations thereof. Somelinkers have pendant side chains or pendant functional groups (or both).Examples of such pendant moieties are hydrophilicity modifiers, forexample, solubilizing groups like, e.g., —SO₃H or —SO₃ ⁻. In someembodiments, a linker may connect a reporter to another moiety such as achemically or enzymatically reactive group (e.g., a cleavable ornon-cleavable terminating moiety). In other embodiments, a linkerconnects a reporter to a biological and non-biological component, forexample, a nucleobase, a nucleoside or a nucleotide. In furtherembodiments, a linker connects chemically reactive groups to anucleobase, a nucleoside or a nucleotide. The moiety formed by a linkerbonded to a reporter may be designated -L-Reporter. Depending on suchfactors as the molecules to be linked and the conditions in which themethod of strand synthesis is performed, the linker may vary in lengthand composition for optimizing properties such as stability, length,FRET efficiency, resistance to certain chemicals and/or temperatureparameters, and be of sufficient stereo-selectivity or size to operablylink a label to a nucleotide such that the resultant conjugate is usefulin optimizing a polymerization reaction. Linkers can be employed usingstandard chemical techniques and include but not limited to, aminelinkers for attaching labels to nucleotides (see, for example, Hobbs andTrainor, U.S. Pat. No. 5,151,507, which is incorporated herein byreference); a linker typically contain a primary or secondary amine foroperably linking a label to a nucleotide; and a rigid hydrocarbon armadded to a nucleotide base (see, for example, Service, 1998, which isincorporated herein by reference). Some exemplary linking methodologiesfor attachment of reporters to base molecules are provided in U.S. Pat.Nos. 4,439,356 and 5,188,934; European Patent Appl. 87310256.0;International Appl. PCT/US90/05565 and Barone et al., 2001, each ofwhich is incorporated herein by reference in its entirety.

A “cleavable linker” is a linker that has one or more cleavable groupsthat may be broken by the result of a reaction or condition. The term“cleavable group” refers to a moiety that allows for release of aportion, e.g., a fluorogenic or fluorescent moiety. Such cleavage istypically chemically, photochemically or enzymatically mediated.Exemplary enzymatically cleavable groups include phosphates, or groupsattached via a peptide bond.

As used herein, the term “IC₅₀” refers to but not limited to theconcentration of a nucleotide analog at which its incorporation on aprimer-template complex yields equal numbers of moles of substrate andproduct and/or could be defined, but not limited to, incorporationefficiency measured by determining the concentration at which thecompound incorporates on half the primer-template complexes.

As used herein, the term “oligonucleotide” refers to DNA fragments of 2to 200 covalently linked nucleotides.

As used herein, the term “reporter” refers to a chemical moiety that isable to produce a detectable signal directly or indirectly. Examples ofreporters include fluorescent dye groups, radioactive labels or groupseffecting a signal through chemiluminescent or bioluminescent means.Examples fluorescent dye groups include zanthene, fluorescein,rhodamine, BODIPY, cyanine, coumarin, pyrene, phthalocyanine,phycobiliprotein, ALEXA FLUOR® 350, ALEXA FLUOR® 405, ALEXA FLUOR® 430,ALEXA FLUOR® 488, ALEXA FLUOR® 514, ALEXA FLUOR® 532, ALEXA FLUOR® 546,ALEXA FLUOR® 555, ALEXA FLUOR® 568, ALEXA FLUOR® 568, ALEXA FLUOR® 594,ALEXA FLUOR® 610, ALEXA FLUOR® 633, ALEXA FLUOR® 647, ALEXA FLUOR® 660,ALEXA FLUOR® 680, ALEXA FLUOR® 700, ALEXA FLUOR® 750, and a squarainedye. Additional examples, of fluorescent dye groups that may be used insome embodiments of the present invention are disclosed throughout thisSpecification and in Haugland, 2005 and U.S. Pat. Nos. 4,439,356 &5,188,934, which are incorporated by reference herein. Examples ofradioactive labels that may be used as reporters in some embodiments ofthe present invention, which are well known in the art such as ³⁵S, ³H,³²P, or ³³P. Examples of reporters that function by chemiluminescent orbioluminescent means and that may be used as reporters in someembodiments of the present invention are described in Nieman, 1989;Given & Schowen, 1989; Orosz et al., 1996; and Hastings, 1983, which areincorporated by reference herein.

As used herein, the term “template” can refer to an oligonucleotideserving as the complimentary strand for DNA synthesis (incorporation) ora recombinant DNA molecule that is made up of a known region, usually avector or adaptor sequence to which a universal primer can bind, and thetarget sequence, which is typically an unknown portion to be sequenced.

The term “fragment templates” refers to a library of fragments that havebeen prepared by randomly shearing genomic DNA into small sizes of <1 kband ligating adaptors to each end of the fragment. These templatesgenerally require less DNA than would be needed for a mate-pair library.

The term “mate-pair templates” refers to a genomic library that hasprepared by circularizing sheared of fragmented DNA that has beenselected for a given size, (examples include 2 kb or 5 kb or 10 kb or 20kb or any other desired size), therefore bringing the ends that werepreviously distant from one another into close proximity. Cutting thesecircles into linear DNA fragments creates mate-pair templates.

As used herein, the term “primer” refers to an oligonucleotide that ishybridized to a complement sequence on the template strand (usually aknown sequence) used to initiate DNA synthesis (incorporation).

When used herein in the scientific or technical sense, the term“incorporation” refers to a nucleotide or nucleotide analog forming acomplement base-pair with the template strand and a covalent bond to aprimer strand by a polymerase. The primer-template complex is extendedone or more bases from the initial primer strand.

As used herein, the term “cleavage” refers to the removal of theterminating group by chemical cleavage, enzymatic cleavage or the like.

As used herein, the term “incorporation cycle” refers to theincorporation of a nucleotide or nucleotide analog by a polymerase, thedetection and identification of said nucleotide or nucleotide analog,and if a nucleotide analog, cleavage of the terminating group and, iforiginally present on the nucleotide analog, fluorescent dye group fromsaid analog.

As used herein, the term “misincorporation” refers to a nucleotide ornucleotide analog forming a non-complement base-pair with the templatestrand and a covalent bond to a primer by a polymerase. Theprimer-template complex is extended one or more bases from the initialprimer strand.

As used herein, the term “discrimination” refers the IC₅₀ concentrationdifferences for misincorporation versus incorporation of nucleotide ornucleotide analogs by a polymerase.

As used herein, the term “termination” refers to the incorporation of anucleotide or nucleotide analog forming a complement or non-complementbase-pair with the template strand and a covalent bond to a primer by apolymerase. The primer-template complex is extended only one base fromthe initial primer strand or growing primer strand for any givenincorporation cycle.

The terms “terminating moiety” and “terminating group” as used herein,are synonymous, referring to a small chemical group (e.g., <500 daltons,excluding any modification, such a linker or linker/dye) that whenattached to at least one part of a nucleoside (i.e., sugar ornucleobase) or nucleotide (i.e., sugar, nucleobase, or phosphate group)confers substantial termination properties to the nucleoside ornucleotide. In some embodiments, the terminating moiety is furthermodified with a linker and/or a linker attached to a dye. In preferredembodiments, the terminating properties of such a modified terminatinggroup is not substantially altered.

As used herein, the term “DT₅₀” refers to the amount of time required tocleavage 50% of the base analog incorporated in the primer-templatecomplex.

The term “analog” as used herein, is understood as being a substancewhich does not comprise the same basic carbon skeleton and carbonfunctionality in its structure as a “given compound”, but which canmimic the given compound by incorporating one or more appropriatesubstitutions such as for example substituting carbon for heteroatoms.

The above definitions supersede any conflicting definition in any of thereference that is incorporated by reference herein. The fact thatcertain terms are defined, however, should not be considered asindicative that any term that is undefined is indefinite. Rather, allterms used are believed to describe the invention in terms such that oneof ordinary skill can appreciate the scope and practice the presentinvention.

V. Examples

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1 Methods and Materials

Reagents and Materials.

All reagents were purchased from commercial sources and used asreceived, unless otherwise noted.

Spectroscopic and Analytical Instrumentation.

¹H NMR, ¹³C NMR, and ³¹P NMR spectra were recorded on a Bruker DPX 400spectrometer as previously described in Wu et al. (2007), which isincorporated herein by reference. Mass spectra analyses were provided bythe Mass Spectrometry Laboratory at the MD Anderson Cancer Center(Houston, Tex.) and the Core Mass Spectrometry Facility at RiceUniversity (Houston, Tex.). X-ray crystallography was performed by theX-ray Diffraction Laboratory at Texas A&M University (College Station,Tex.). UV/Vis measurements were taken using a Beckman DU-800spectrophotometer. Anion exchange chromatography was performed using a QSepharose FF column (2.5×20 cm) with a linear gradient of 75%triethylammonium bicarbonate (TEAB, 0.1 M) in 25% acetonitrile to 75%TEAB (1.5 M) in 25% acetonitrile over 240 min at a flow rate of 4.5 mLper min. Reverse-phase high performance liquid chromatography (RP-HPLC)was performed using a Beckman System Gold equipped with a 128 solventmodule and 166 UV detector or 168 photodiode array UV/Vis detector.RP-HPLC for nucleosides and nucleotide analogs was performed using a 4.6mm×250 mm Aquapore OD-300 C₁₈ column, with buffer A containing 100 mMtriethylammonium acetate (TEAA), pH 7.0, and buffer B containing 100 mMTEAA, pH 7.0, 70% acetonitrile (v/v).

Example 2 Synthesis of α-Substituted 2-Nitrobenzyl Alcohols(R/S)-1-(2-Nitrophenyl)-2-methyl-1-propanol

Synthesis of (R/S)-1-(2-nitrophenyl)-2-methyl-1-propanol was previouslyreported. See Litosh et al. (2011), which is incorporated herein byreference.

(R/S)-1-(2-Nitrophenyl)-2,2-dimethyl-1-propanol

Synthesis of (R/S)-1-(2-nitrophenyl)-2,2-dimethyl-1-propanol waspreviously reported. See Litosh et al. (2011), which is incorporatedherein by reference.

(R/S)-1-(2,6-Dinitrophenyl)-2-methyl-1-propanol

To a solution of 1-iodo-2,6-dinitrobenzene (Smith and Ho, 1990), whichis incorporated herein by reference) (1.55 g, 5.27 mmol) in anhydrousTHF (18 mL) at minus 50° C. under a nitrogen atmosphere, phenylmagnesiumbromide (2 M in THF, 3.2 mL, 6.4 mmol) was added dropwise at a rate suchthat the temperature would not exceed minus 45° C. Upon completion ofthe addition, the mixture was stirred at minus 50° C. for five min,followed by addition of isobutyraldehyde (0.96 mL, 11 mmol). The mixturewas gradually warmed up to room temperature, quenched with saturatedNH₄Cl solution (10 mL), and then diluted with water (50 mL). The mixturewas extracted with CH₂Cl₂ (100 mL) three times. The combined organicphase was washed with brine (50 mL), dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel column chromatographyto yield (R/S)-1-(2,6-dinitrophenyl)-2-methyl-1-propanol (0.375 g, 30%)as a yellow oil. ¹H NMR (400 MHz, CDCl₃): δ 7.82 (d, 2H, J=8.0 Hz,Ph-H), 7.59 (t, 1H, J=8.0 Hz, Ph-H), 4.83 (dd, 1H, J=9.2 and 7.6 Hz,Ph-CH), 2.87 (d, 1H, J=7.6 Hz, OH), 2.19 (m, 1H, CH), 1.12 (d, 3H, J=6.4Hz, CH₃), 0.76 (d, 3H, J=6.8 Hz, CH₃).

(R/S)-1-(4-Methoxy-2-nitrophenyl)-2-methyl-1-propanol

To a solution of 4-iodo-3-nitroanisole (2.79 g, 10.0 mmol) in anhydrousTHF (20 mL) at minus 40° C. under a nitrogen atmosphere, phenylmagnesiumchloride (2 M in THF, 6.0 mL, 12 mmol) was added dropwise at a rate suchthat the temperature would not exceed minus 35° C. Upon completion ofthe addition, the mixture was stirred at minus 40° C. for five min,followed by addition of isobutyraldehyde (1.8 mL, 20 mmol). The mixturewas gradually warmed to room temperature, quenched with saturated NH₄Clsolution (5.0 mL), diluted with CH₂Cl₂ (100 mL) and washed with water(100 mL). The organic phase was separated, and the aqueous phase wasextracted with CH₂Cl₂ (50 mL) three times. The combined organic phasewas washed with brine (40 mL), dried over Na₂SO₄, concentrated in vacuo,and the residue was purified by silica gel column chromatography toyield (R/S)-1-(4-methoxy-2-nitrophenyl)-2-methyl-1-propanol (1.5 g, 67%)as a light yellow oil. ¹H NMR (400 MHz, CDCl₃): δ 7.61 (d, 1H, J=8.8 Hz,Ph-H), 7.34 (d, 1H, J=2.8 Hz, Ph-H), 7.15 (dd, 1H, J=8.8 and 2.8 Hz,Ph-H), 4.92 (dd, 1H, J=5.6 and 3.2 Hz, Ph-CH), 2.46 (br s, 1H, OH), 2.00(m, 1H, CH), 0.97 (d, 3H, J=6.4 Hz, CH₃), 0.86 (d, 3H, J=6.8 Hz, CH₃).

(R/S)-1-(4-Methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol

To a solution of 4-iodo-3-nitroanisole (2.38 g, 8.50 mmol) in anhydrousTHF (10 mL) at minus 40° C. under a nitrogen atmosphere, phenylmagnesiumchloride (2 M in THF, 4.7 mL, 9.4 mmol) was added dropwise at a ratesuch that the temperature would not exceed minus 35° C. Upon completionof the addition, the mixture was stirred at minus 40° C. for one hour,followed by addition of trimethylacetaldehyde (1.13 mL, 10.2 mmol). Themixture was stirred at minus 40° C. for two hours and then at roomtemperature for another one hour. The reaction was quenched with brine(100 mL), and the mixture was extracted with CH₂Cl₂ (40 mL) three times.The combined organic phase was dried over Na₂SO₄ and concentrated invacuo, and the residue was purified by silica gel column chromatographyto yield racemic(R/S)-1-(4-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (1.52 g, 74%).¹H NMR (400 MHz, CDCl₃): δ 7.67 (d, 1H, J=9.2 Hz, Ph-H), 7.22 (d, 1H,J=2.4 Hz, Ph-H), 7.12 (dd, 1H, J=8.8 and 2.8 Hz, Ph-H), 5.27 (d, 1H,J=4.0 Hz, Ph-CH), 3.86 (s, 3H, OCH₃), 2.01 (d, 1H, J=4.0 Hz, OH), 0.86(s, 9H, C(CH₃)₃).

(R/S)-1-(5-Methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol and(S)-1-(5-methoxy-2-nitro-phenyl)-2,2-dimethyl-1-propanol

To a solution of 3-iodo-4-nitroanisole (2.79 g, 10.0 mmol) in anhydrousTHF (10 mL) at minus 40° C. under a nitrogen atmosphere, phenylmagnesiumchloride (2 M in THF, 4.2 mL, 8.3 mmol) was added dropwise at a ratesuch that the temperature would not exceed minus 35° C. Upon completionof the addition, the mixture was stirred at minus 40° C. for two hours,followed by addition of trimethylacetaldehyde (1.1 mL, 10 mmol). Themixture was stirred at minus 40° C. for two hours and then at roomtemperature for another one hour. The reaction was then quenched withbrine (100 mL), and the mixture was extracted with CH₂Cl₂ (40 mL) threetimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel column chromatographyto yield racemic(R/S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (1.76 g, 88%).¹H NMR (400 MHz, CDCl₃): δ 7.89 (d, 1H, J=9.2 Hz, Ph-H), 7.27 (d, 1H,J=2.8 Hz, Ph-H), 6.84 (dd, 1H, J=8.8 and 2.8 Hz, Ph-H), 5.62 (d, 1H,J=4.0 Hz, PhCH), 3.89 (s, 3H, OCH₃), 2.08 (d, 1H, J=4.0 Hz, OH), 0.89(s, 9H, C(CH₃)₃).

To a solution of racemic(R/S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (1.75 g, 7.3mmol) and DMAP (2.92 g, 23.9 mmol) in anhydrous CH₂Cl₂ (10 mL),(1S)-camphanic chloride (Corrie et al., 1992), which is incorporated byreference) (2.6 g, 12 mmol) was added, and the mixture was stirredovernight at room temperature under a nitrogen atmosphere. The reactionmixture was diluted with CH₂Cl₂ (50 mL) and washed with saturated NaHCO₃solution (50 mL). The organic phase was dried over Na₂SO₄, concentratedin vacuo, and the residue was purified by silica gel columnchromatography to yield(R/S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl (1S)-camphanate(2.5 g, 85%, 1:1 mixture of diastereomers). The camphanate was dissolvedin ethyl acetate (30 mL) followed by slow addition of hexane (120 mL)with stirring. Needle crystals formed gradually from the solution over atwo-hour period. The crystals were collected by filtration to yield puresingle diastereomer(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl (1S)-camphanate.The filtrate was concentrated in vacuo, and the crystallization processwas repeated twice to provide additional(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl (1S)-camphanate(total 1.08 g, 43%). ¹H NMR (400 MHz, CDCl₃): δ 8.04 (d, 1H, J=9.2 Hz,Ph-H), 7.27 (d, 1H, J=2.8 Hz, Ph-H), 6.88 (dd, 1H, J=2.8 and 8.8 Hz,Ph-H), 6.81 (3, 1H, Ph-CH), 3.87 (s, 3H, OCH₃), 2.36 (m, 1H, CH), 1.92(m, 2H, CH₂), 1.66 (m, 1H, CH), 1.12 (s, 3H, CH₃), 1.06 (s, 3H, CH₃),1.02 (s, 3H, CH₃), 0.95 (s, 9H, C(CH₃)₃).

Method for Obtaining X-Ray Crystallography Data:

Crystallographic measurements were made on a crystal of(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl (1S)-camphanatewith dimensions of 0.50 mm×0.05 mm×0.05 mm as described by Litosh et at(2011), which is incorporated herein by reference. See FIG. 3.

Data Collection:

CuKα radiation, λ=1.54178 Å, T=110±2° K, 2θ=120.0°, 32,513 reflectionscollected, 2,913 unique (R_(int)=0.0517). Final GooF=1.091, R1=0.0681,wR2=0.1695, R indices based on 2,913 reflections with I>2sigma(I)(refinement on F²), 290 parameters, 43 restraints. Lp and absorptioncorrections applied, μ=0.819 mm⁻¹. Absolute structure parameter:0.05±0.09.

X-Ray Crystallography Data:

C₂₂H₂₉NO₇, M=419.46. Orthorhombic, a=6.29, b=15.00, c=22.27 Å (α, β,γ=90°), V=2,099.29 Å³, space group P2₁2₁2₁, Z=4, D_(c)=1.327 g/cm⁻³,F(000)=896.

A mixture of (S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (590 mg, 1.4 mmol) and K₂CO₃ (389 mg, 2.8 mmol) inmethanol (MeOH, 25 mL) was heated to reflux for one hour, then cooleddown, concentrated in vacuo, and diluted with CH₂Cl₂ (50 mL). Theorganic phase was washed with brine (50 mL), dried over Na₂SO₄,concentrated in vacuo, and the residue was purified by silica gel columnchromatography to yield enantiopure(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (333 mg, 99%).¹H NMR was identical with that of the racemic alcohol.

(R/S)-1-(4,5-Dimethoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol

1,2-Dimethoxybenzene (5.0 g, 36 mmol) was dissolved in acetic acid (10mL), and the solution was cooled in an ice-water bath followed bydropwise addition of iodine chloride (8.7 g, 54 mmol). After 10 min, thereaction mixture was heated to 100° C. for two hours and then cooled toroom temperature. Needle crystals that precipitated from solution werefiltered and washed with acetic acid (5.0 mL) three times. The crystalswere dried overnight under high vacuum to yield4,5-diiodo-1,2-dimethoxybenzene (8.8 g, 62%). NMR (400 MHz, CDCl₃): δ7.28 (s, 2H, Ph-H), 3.85 (s, 6H, OCH₃).

4,5-Diiodo-1,2-dimethoxybenzene (8.8 g, 23 mmol) was added into aceticacid (300 mL), and the mixture was heated to 100° C. to dissolve thesolid. The clear mixture was then cooled to room temperature followed bydropwise addition of nitric acid (68-70%, 120 mL). The reaction mixturewas stirred at room temperature overnight and then poured into ice-water(200 mL). The mixture was extracted by CH₂Cl₂ (100 mL) three times. Thecombined organic phase was washed with saturated NaHCO₃ solution (200mL), brine (100 mL), and dried over Na₂SO₄, concentrated in vacuo, andthe residue was purified by silica gel column chromatography to yield4-iodo-5-nitro-1,2-dimethoxybenzene (5.25 g, 75%). ¹H NMR (400 MHz,CDCl₃): δ 7.60 (s, 1H, Ph-H), 7.38 (s, 1H, Ph-H), 3.98 (s, 3H, OCH₃),3.92 (s, 3H, OCH₃).

To a solution of 4-iodo-5-nitro-1,2-dimethoxybenzene (4.6 g, 15 mmol) inanhydrous THF (10 mL) at minus 40° C. under a nitrogen atmosphere,phenylmagnesium chloride (2 M in THF, 7.5 mL, 15 mmol) was addeddropwise at a rate such that the temperature would not exceed minus 35°C. Upon completion of the addition, the mixture was stirred at minus 40°C. for two hours, followed by addition of trimethyl acetaldehyde (2.0mL, 18 mmol). The mixture was stirred at minus 40° C. for two hours andthen at room temperature for another one hour. The reaction was quenchedwith brine (100 mL), and the mixture was extracted with CH₂Cl₂ (40 mL)three times. The combined organic phase was dried over Na₂SO₄ andconcentrated in vacuo, and the residue was purified by silica gel columnchromatography to yield racemic(R/S)-1-(4,5-dimethoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (0.8 g,20%). ¹H NMR (400 MHz, CDCl₃): δ 7.41 (1, 1H, Ph-H), 7.21 (s, 1H, Ph-H),5.60 (s, 1H, PhCH), 3.95 (s, 3H, OCH₃), 3.92 (s, 3H, OCH₃), 0.90 (s, 9H,(CH₃)₃).

Example 3 Synthesis of 7-HOMe-7-Deaza-2′-Deoxyadenosine TriphosphateAnalogs7-(2-nitrobenzyloxy)methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate

Compound 1 (Seela et al. (2005), which is incorporated herein byreference), (0.79 g, 2.0 mmol) was evaporated from anhydrous pyridine(2.0 mL) three times and dissolved in anhydrous DMF (4.0 mL).tert-Butyldimethylsilyl chloride (0.90 g, 6.0 mmol) and imidazole (0.82g, 12 mmol) were added, and the mixture was stirred at room temperaturefor 16 hours. The reaction was concentrated in vacuo and purified bysilica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-6-chloro-7-iodo-7-deazapurine2 (1.08 g, 87%) as a white foam. ¹H NMR (400 MHz, CDCl₃): δ 8.61 (s, 1H,H-2), 7.81 (s, 1H, H-8), 6.74 (t, 1H, J=6.4 Hz, H-1′), 4.56 (m, 1H,H-4′), 4.01 (m, 1H, H-3′), 3.87 (dd, 1H, H-5′a), 3.79 (dd, 1H, H-5′b),2.39 (m, 2H, H-2′a and H-2′b), 0.96 (s, 9H, (CH₃)₃CSi), 0.91 (s, 9H,(CH₃)₃CSi), 0.18 (2s, 6H, (CH₃)₂Si), 0.15 (s, 6H, (CH₃)₂Si).

To a solution of compound 2 (1.55 g, 2.48 mmol) in anhydrous 1,4-dioxane(42 mL) and anhydrous MeOH (42 mL), triethylamine (0.87 mL) was added.After stirring for 10 min under a CO atmosphere,bis(benzonitrile)dichloropalladium(II) (0.05 g, 0.13 mmol) was added,and the reaction was stirred at 50° C. for 48 hours under a COatmosphere. The mixture was then concentrated in vacuo, and the residuewas purified by silica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-6-chloro-7-methoxycarbonyl-7-deazapurine3 (1.36 g, 98%) as a viscous oil. ¹H NMR (400 MHz, CDCl₃): δ 8.69 (s,1H, H-2), 8.31 (s, 1H, H-8), 6.77 (t, 1H, J=6.8 Hz, H-1′), 4.58 (m, 1H,H-4′), 4.06 (m, 1H, H-3′), 3.90 (s, 3H, CH₃O), 3.87 (dd, 1H, H-5′a),3.81 (dd, 1H, H-5′b), 2.42 (m, 2H, H-2′a and H-2′b), 0.93 (s, 18H,(CH₃)₃CSi), 0.13 (s, 6H, (CH₃)₂Si), 0.12 (s, 6H, (CH₃)₂Si).

To a solution of compound 3 (0.28 g, 0.50 mmol) in anhydrous THF (4.0mL), lithium borohydride (44 mg, 2.0 mmol) was added, followed by MeOH(0.1 mL). The reaction mixture was stirred at room temperature for 10min and then heated to reflux for 45 min. Upon cooling to roomtemperature, the mixture was diluted with CH₂Cl₂ (20 mL) and water (2.0mL). The organic layer was separated, washed with brine (5.0 mL) twotimes, dried over Na₂SO₄, and concentrated in vacuo. The residue waspurified by silica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-6-chloro-7-hydroxymethyl-7-deazapurine4 (0.12 g, 45%) as a white foam. ¹H NMR (400 MHz, CDCl₃): δ 8.62 (s, 1H,H-8), 7.61 (s, 1H, H-2), 6.75 (dd, 1H, J=6.0 and 7.2 Hz, H-1′), 4.96 (ABd, 1H, J=11.6 Hz, 7-CH₂a), 4.91 (AB d, 1H, J=11.6 Hz, 7-CH₂b), 4.57 (m,1H, H-4′), 4.00 (m, 1H, H-3′), 3.80 (m, 2H, H-5′a and H-5′b), 2.44 (m,1H, H-2′a), 2.04 (m, 1H, H-2′b), 0.91 (2 s, 18H, (CH₃)₃CSi), 0.11 (2 s,12H, (CH₃)₂Si).

To a solution of compound 4 (30 mg, 0.057 mmol) in CH₂Cl₂ (2.0 mL),n-Bu₄NBr (9 mg, 0.029 mmol), 2-nitrobenzyl bromide (37 mg, 0.17 mmol)and NaOH solution (1 M, 2.0 mL) were added. The reaction mixture wasstirred vigorously at room temperature for 48 hours in the dark. Theorganic layer was separated, dried over Na₂SO₄, concentrated in vacuo,and the residue was purified by silica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-6-chloro-7-(2-nitrobenzyloxy)methyl-7-deazapurine5 (19 mg, 50%) as a viscous oil. ¹H NMR (400 MHz, CDCl₃): δ 8.63 (s, 1H,H-2), 8.06 (dd, 1H, J=8.4 and 1.2 Hz, Ph-H), 7.84 (d, 1H, J=7.6 Hz,Ph-H), 7.64 (s, 1H, H-8), 7.62 (m, 1H, Ph-H), 7.43 (t, 1H, Ph-H), 6.75(dd, 1H, J=7.2 and 6.0 Hz, H-1′), 5.03 (s, 2H, PhCH₂), 4.95 (AB d, 1H,J=12.0 Hz, 7-CH₂a), 4.88 (AB d, 1H, J=12.0 Hz, 7-CH₂b), 4.59 (m, 1H,H-4′), 4.00 (m, 1H, H-3′), 3.80 (m, 2H, H-5′a and H-5′b), 2.48 (m, 1H,H-2′a), 2.37 (m, 1H, H-2′b), 0.92 (2 s, 18H, (CH₃)₃CSi), 0.11 (s, 6H,(CH₃)₂Si), 0.10 (s, 6H, (CH₃)₂Si).

A solution of n-Bu₄NF (17 mg, 0.054 mmol) in THF (1.0 mL) was added to asolution of compound 5 (18 mg, 0.028 mmol) in THF (1.0 mL) at 0° C. Thereaction mixture was gradually warmed to room temperature and stirredfor two hours. The mixture was concentrated in vacuo, dissolved in1,4-dioxane (2.0 mL), followed by addition of NH₃ in MeOH solution (7 M,4.0 mL). The mixture was transferred to a sealed tube and stirred at100° C. for 16 hours, then cooled to room temperature, concentrated invacuo, and the residue was purified by silica gel chromatography toyield 7-(2-nitrobenzyloxyl)methyl-7-deaza-2′-deoxyadenosine 6 (10 mg,91%) as a white foam. ¹H NMR (400 MHz, DMSO-d₆): δ 8.08 (s, 1H, H-2),8.06 (m, 1H, Ph-H), 7.75 (m, 2H, Ph-H), 7.58 (m, 1H, Ph-H), 7.42 (s, 1H,H-8), 6.64 (bs, 2H, D₂O exchangeable, 6-NH₂), 6.48 (dd, 1H, J=2.0 and6.0 Hz, H-1′), 5.25 (d, 1H, J=4.0 Hz, D₂O exchangeable, 3′-OH), 5.08 (t,1H, J=5.6 Hz, D₂O exchangeable, 5′-OH), 4.90 (s, 2H, PhCH₂), 4.75 (ABdd, 2H, 7-CH₂), 4.33 (m, 1H, H-3′), 3.81 (m, 1H, H-4′), 3.54 (m, 2H,H-5′a and H-5′b), 2.47 (m, 1H, H-2′a), 2.15 (m, 1H, H-2′b).

Compound 6 (6 mg, 0.014 mmol) was phosphorylated with POCl₃ (2.6 μL,0.028 mmol) and proton sponge (6 mg, 0.028 mmol) in trimethylphosphate(0.25 mL) at minus 40° C. for four hours under a nitrogen atmosphere. Asolution of bis-tri-n-butylammonium pyrophosphate (66 mg, 0.14 mmol) andtri-n-butylamine (28 μL) in anhydrous DMF (0.28 mL) was added. After 30min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 1.0mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in water (2.0mL), filtered, and purified using RP-HPLC (see above) to yield7-(2-nitro-benzyloxy)methyl-7-deaza-2′-deoxyadenosine-5′-triphosphatedA.I. HRMS (ESI): For the molecular ion C₁₉H₂₃N₅O₁₅P₃ [M−H]⁻, thecalculated mass was 654.0403, and the observed mass was 654.0397.

7-[1-(2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate

To a solution of compound 4 (0.26 g, 0.49 mmol) in anhydrous CH₂Cl₂ (12mL), 4-dimethylaminopyridine (DMAP; 0.15 g, 1.2 mmol) and tosyl chloride(0.11 g, 0.58 mmol) were added. The reaction mixture was stirred at roomtemperature for 18 hours and then concentrated in vacuo. The residue waspurified by silica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-6-chloro-7-chloromethyl-7-deazapurine7 (0.103 g, 39%) as a viscous oil. ¹H NMR (400 MHz, CDCl₃): δ 8.64 (s,1H, H-2), 7.72 (s, 1H, H-8), 6.73 (t, 1H, J=6.8 Hz, H-1′), 4.95 (AB d,J=12.4 Hz, 7-CH_(2a)), 4.91 (AB d, J=12.0 Hz, 7-CH_(2b)), 4.58 (m, 1H,H-3′), 4.00 (m, 1H, H-4′), 3.82 (m, 2H, H-5′a and H-5′b), 2.41 (m, 2H,H-2′a and H-2′b), 0.95 (s, 9H, (CH₃)₃CSi), 0.93 (s, 9H, (CH₃)₃CSi), 0.12(s, 6H, (CH₃)₂Si), 0.11 (s, 6H, (CH₃)₂Si).

Compound 7 (54 mg, 0.10 mmol) and racemic(R/S)-1-(2-nitrophenyl)-2-methyl-propanol (191 mg, 0.98 mmol) weredissolved in anhydrous CH₂Cl₂ (10 mL). The solvent was removed in vacuo,and the residue was heated for one hour under a nitrogen atmosphere,then dissolved in minimum amount of ethyl acetate and purified by silicagel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxy-ribofuranosyl]-6-chloro-7-[1-(2-nitro-phenyl)-2-methyl-propyloxy]methyl-7-deazapurine8 (38 mg, 54%) as a 1:1 mixture of two diastereomers. ¹H NMR (400 MHz,CDCl₃) for diastereomers: δ 8.60 and 8.59 (2 s, 1H, H-2), 7.83 (m, 1H,Ph-H), 7.79 (m, 1H, Ph-H), 7.56 (m, 1H, Ph-H), 7.48 and 7.47 (2 s, 1H,H-8), 7.38 (m, 1H, Ph-H), 6.70 (m, 1H, H-1′), 4.81 (m, 1H, Ph-CH), 4.70(m, 1H, 7-CH₂a), 4.58 (m, 2H, 7-CH₂b and H-3′), 3.99 (m, 1H, H-4′), 3.78(m, 2H, H-5′a and H-5′b), 2.48 (m, 1H, H-2′a), 2.35 (m, 1H, H-2′b), 1.96(m, 1H, CH), 0.98 and 0.96 (2 d, 3H, CH₃), 0.93 (2 s, 9H, (CH₃)₃CSi),0.89 (2 s, 9H, (CH₃)₃CSi), 0.82 and 0.78 (2 d, 3H, CH₃), 0.12 (2 s, 6H,(CH₃)₂Si), 0.08 and 0.07 (2 s, 3H, (CH₃)₂Si), 0.06 and 0.05 (2 s, 3H,(CH₃)₂Si).

A solution of n-Bu₄NF (44 mg, 0.14 mmol) in THF (2.0 mL) was added to asolution of compound 8 (38 mg, 0.05 mmol) in THF (2.0 mL) at 0° C. Thereaction was gradually warmed to room temperature and stirred for twohours. The mixture was concentrated in vacuo, dissolved in 1,4-dioxane(4.0 mL), followed by addition of NH₃ in MeOH solution (7 M, 8.0 mL).The mixture was transferred to a sealed tube, stirred at 100° C. for 24hours, cooled to room temperature, and then concentrated in vacuo. Theresidue was purified by silica gel chromatography to yield7-[1-(2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine9 (19 mg, 76%) as a 1:1 mixture of two diastereomers. ¹H NMR (400 MHz,DMSO-d₆) for diastereomers: δ 8.06 and 8.04 (2 s, 1H, H-2), 7.90 (m, 1H,Ph-H), 7.67 (m, 2H, Ph-H), 7.56 (m, 2H, Ph-H), 7.19 and 7.16 (2 s, 1H,H-8), 6.63 (bs, 2H, D₂O exchangeable, 6-NH₂), 6.39 (m, 1H, H-1′), 5.23(m, 1H, D₂O exchangeable, 3′-OH), 5.00 (m, 1H, D₂O exchangeable, 5′-OH),4.72 (2 d, 1H, Ph-CH), 4.45 (s, 2H, 7-CH₂), 4.30 (m, 1H, H-3′), 3.77 (m,1H, H-4′), 3.49 (m, 2H, H-5′a and H-5′b), 2.40 (m, 1H, H-2′a), 2.12 (m,1H, H-2′b), 1.94 (m, 1H, CH), 0.87 (m, 3H, CH₃), 0.74 (m, 3H, CH₃).

Compound 9 (19 mg, 0.041 mmol) was phosphorylated with POCl₃ (16 μL,0.16 mmol) and proton sponge (18 mg, 0.082 mmol) in trimethylphosphate(0.4 mL) at minus 40° C. for five hours under a nitrogen atmosphere. Asolution of bis-tri-n-butylammonium pyrophosphate (97 mg, 0.20 mmol) andtri-n-butylamine (40 μL) in anhydrous DMF (0.40 mL) was added. After 30min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in water (5.0mL), filtered, and purified by anion exchange chromatography. Thefractions containing triphosphate were combined and lyophilized to yield7-[1-(2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphatedA.III.a as a 1:1 mixture of two diastereomers, which were separatedusing RP-HPLC to yield the single diastereomers dA.III.a ds1 anddA.III.a ds2. In all cases, diastereomer 1 (ds1) eluted faster thandiastereomer 2 (ds2) by RP-HPLC. HRMS (ESI): For the molecular ionC₂₂H₂₉N₅O₁₅P₃ [M−H]⁻, the calculated mass was 696.0873, and the observedmass was 696.0864.

7-[1-(4-Methoxy-2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate

Compound 7 (103 mg, 0.19 mmol) and racemic(R/S)-1-(4-methoxy-2-nitrophenyl)-2-methyl-1-propanol (428 mg, 1.9 mmol)were dissolved in anhydrous CH₂Cl₂ (3.0 mL). The solvent was removed invacuo, and the residue was heated at 108° C. for 30 min under a nitrogenatmosphere, cooled to room temperature, dissolved in minimum amount ofethyl acetate, and purified by silica gel chromatography to yield6-chloro-7-[1-(4-methoxy-2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deazapurine2′-deoxyribonucleosides 10. The sample was dissolved in THF (8.0 mL),cooled to 0° C., and then added to a solution of n-Bu₄NF (68 mg, 0.22mmol) in THF (2.0 mL). The reaction was gradually warmed to roomtemperature and stirred for 30 min. The mixture was concentrated invacuo, dissolved in 1,4-dioxane (8.0 mL), followed by addition of NH₃ inMeOH (7 N, 24 mL). The mixture was transferred to a sealed tube andstirred at 100° C. for 16 hours, then cooled to room temperature, andconcentrated in vacuo. The residue was purified by silica gelchromatography to yield7-[1-(4-methoxy-2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine11 (30 mg, 32% for three steps) as a 1:1 mixture of two diastereomers.¹H NMR (400 MHz, DMSO-d₆) for diastereomers: δ 8.06 and 8.05 (2 s, 1H,H-2), 7.57 and 7.54 (2 d, 1H, J=8.8 Hz, Ph-H), 7.47 and 7.44 (2 d, 1H,J=2.6 Hz, Ph-H), 7.33 and 7.27 (2 dd, J=8.8 and 2.6 Hz, 1 H, Ph-H), 7.18and 7.15 (2 s, 1H, H-8), 6.63 (bs, 2H, D₂O exchangeable, 6-NH₂), 6.43(m, 1H, H-1′), 5.24 (m, 1H, D₂O exchangeable, 3′-OH), 5.03 (m, 1H, D₂Oexchangeable, 5′-OH), 4.55 (m, 2H, Ph-CH, 7-CH₂a), 4.30 (m, 2H, 7-CH₂band H-3′), 3.86 and 3.84 (2 s, 3H, MeO), 3.78 (m, 1H, H-4′), 3.48 (m,2H, H-5′), 2.45 (m, 1H, H-2′a), 2.12 (m, 1H, H-2′b), 1.93 (m, 1H,CH(CH₃)₂), 0.88 (m, 3H, CH₃), 0.74 and 0.71 (2 d, J=6.8 Hz, 3H, CH₃).

Compound 11 (28 mg, 0.06 mmol) was phosphorylated with POCl₃ (11 μL,0.12 mmol) and proton sponge (25 mg, 0.12 mmol) in trimethylphosphate(0.35 mL) at 0° C. for two hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (10 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to yield7-[1-(4-methoxy-2-nitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphatedA.III.b as a 1:1 mixture of two diastereomers, which were separatedusing RP-HPLC to yield the single diastereomers dA.III.b ds1 anddA.III.b ds2. HRMS (ESI): For the molecular ion C₂₃H₃₁N₅O₁₆P₃ [M−H]⁻,the calculated mass was 726.0979, and the observed mass was 726.0984.

7-[1-(2,6-Dinitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate

Compound 7 (109 mg, 0.20 mmol) and racemic(R/S)-1-(2,6-dinitrophenyl)-2-methyl-1-propanol (448 mg, 1.9 mmol) weredissolved in anhydrous CH₂Cl₂ (10 mL). The solvent was removed in vacuo,and the residue was heated at 108° C. for 30 min under a nitrogenatmosphere, then dissolved in minimum amount of ethyl acetate andpurified by silica gel chromatography to yield6-chloro-7-[1-(2,6-dinitrophenyl)-2-methyl-propyloxy]methyl-7-deazapurine-2′-deoxyribo-nucleosides12. The sample was dissolved in THF (5.0 mL), cooled to 0° C., and thenadded a solution of n-Bu₄NF (31 mg, 0.10 mmol) in THF (2.0 mL). Thereaction was gradually warmed to room temperature and stirred for twohours. The mixture was concentrated in vacuo, dissolved in 1,4-dioxane(4.0 mL), followed by addition of NH₃ in MeOH (7 N, 18 mL). The mixturewas transferred to a sealed tube, stirred at 100° C. for 36 hours,cooled to room temperature, and then concentrated in vacuo. The residuewas purified by silica gel chromatography to yield7-[1-(2,6-dinitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine13 (38 mg, 38% for three steps) as a 1:1 mixture of two diastereomers.¹H NMR (400 MHz, DMSO-d₆) for diastereomers: δ 8.17 (m, 1H, Ph-H), 8.07and 8.06 (2 s, 1H, H-2), 7.85 (m, 1H, Ph-H), 7.69 (m, 1H, Ph-H), 7.20and 7.18 (2 s, 1H, H-8), 6.57 (bs, 2H, D₂O exchangeable, 6-NH₂), 6.46(m, 1H, H-1′), 5.26 (d, J=3.6 Hz, 1H, D₂O exchangeable, 3′-OH), 5.01 (m,1H, D₂O exchangeable, 5′-OH), 4.60 (m, 2H, Ph-CH and 7-CH₂a), 4.29 (m,1H, 7-CH₂b), 4.13 (m, 1H, H-3′), 3.80 (m, 1H, H-4′), 3.51 (m, 2H, H-5′aand H-5′b), 2.49 (m, 1H, CH(CH₃)₃), 2.16 (m, 2H, H-2′a and H-2′b), 0.91(m, 3H, CH₃), 0.65 (m, 3H, CH₃). ToF-MS (ESI): For the molecular ionC₂₂H₂₇N₆O₈ [M+H]⁻, the calculated mass was 503.1890, and the observedmass was 503.2029.

Compound 13 (30 mg, 0.06 mmol) was phosphorylated with POCl₃ (17 μL,0.18 mmol) and proton sponge (26 mg, 0.12 mmol) in trimethylphosphate(0.4 mL) at 0° C. for four hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (285 mg, 0.6 mmol) andtri-n-butylamine (120 μL) in anhydrous DMF (1.2 mL) was added. After 30min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 10mL) was added. The reaction was stirred for one hour at room temperatureand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (10 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to yield7-[1-(2,6-dinitrophenyl)-2-methyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphatedA.III.c as a 1:1 mixture of two diastereomers which were separatedusing RP-HPLC to yield the single diastereomers dA.III.c ds1 anddA.III.c ds2. HRMS (ESI): For the molecular ion C₂₂H₂₈N₆O₁₇P₃ [M−H]⁻,the calculated mass was 741.0724, and the observed mass was 741.0731.

7-[(S)-1-(2-Nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate

Compound 7 (130 mg, 0.24 mmol) and(S)-1-(2-nitrophenyl)-2,2-dimethyl-1-propanol (290 mg, 1.4 mmol) wereheated at 110° C. for 45 min under a nitrogen atmosphere. The reactionmixture was cooled to room temperature and dissolved in THF (10 mL)followed by addition of n-Bu₄NF (189 mg, 0.60 mmol). The mixture wasstirred at room temperature for two hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (20 mL) and washed with brine(30 mL), and the aqueous phase was extracted with CH₂Cl₂ (20 mL) twotimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine14 (90 mg, 75%). ¹H NMR (400 MHz, CDCl₃): δ 8.51 (s, 1H, H-2), 7.68 (m,2H, Ph-H), 7.45 (t, 1H, J=7.2 Hz, Ph-H), 7.38 (s, 1H, H-8), 7.29 (t, 1H,J=7.2 Hz, Ph-H), 6.39 (dd, 1H, J=6.0 and 8.0 Hz, H-1′), 4.97 (s, 1H,Ph-CH), 4.70 (m, 3H, 7-CH₂ and H-3′), 4.16 (m, 1H, H-4′), 3.83 (m, 2H,H-5′), 2.80 (m, 1H, H-2′a), 2.35 (m, 1H, H-2′b), 0.82 (s, 9H, C(CH₃)₃).

Compound 14 (90 mg, 0.18 mmol) was dissolved in 1,4-dioxane (8.0 mL)followed by addition of NH₃ in MeOH (7 N, 16 mL). The mixture wastransferred to a sealed tube and stirred at 100° C. for 24 hours, cooledto room temperature, and then concentrated in vacuo. The residue waspurified by silica gel chromatography to yield7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine15 (80 mg, 93%). ¹H NMR (400 MHz, DMSO-d₆): δ 8.09 (s, 1H, H-2), 7.91(dd, 1H, J=1.2 and 8.0 Hz, Ph-H), 7.71 (m, 2H, Ph-H), 7.58 (m, 1H,Ph-H), 7.24 (s, 1H, H-8), 6.68 (bs, 2H, D₂O exchangeable, 6-NH₂), 6.46(dd, 1H, J=6.0 and 8.0 Hz, H-1′), 5.27 (d, 1H, D₂O exchangeable, 3′-OH),5.06 (t, 1H, D₂O exchangeable, 5′-OH), 4.87 (s, 1H, Ph-CH), 4.65 (d, 1H,J=12.8 Hz, 7-CH₂a), 4.49 (m, 1H, H-3′), 4.36 (d, 1H, 7-CH₂b), 3.80 (m,1H, H-4′), 3.49 (m, 2H, H-5′), 2.45 (m, 1H, H-2′a), 2.17 (m, 1H, H-2′b),0.75 (s, 9H, C(CH₃)₃).

Compound 15 (25 mg, 0.053 mmol) was phosphorylated with POCl₃ (22 μL,0.24 mmol) and proton sponge (23 mg, 0.11 mmol) in trimethylphosphate(0.35 mL) at 0° C. for 4.5 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to yield7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphatedA.V, which was further purified using RP-HPLC. HRMS (ESI): For themolecular ion C₂₃H₃₁N₅O₁₅P₃ [M−H]⁻, the calculated mass was 710.1029,and the observed mass was 710.1032.

7-[(S)-1-(5-Methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate

Compound 7 (165 mg, 0.30 mmol) and(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (330 mg, 1.4mmol) were heated at 110° C. for 45 min under a nitrogen atmosphere. Thereaction mixture was cooled to room temperature and dissolved in THF (10mL), followed by addition of n-Bu₄NF (236 mg, 0.75 mmol). The mixturewas stirred at room temperature for two hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (40 mL) and washed with brine(50 mL), and the aqueous phase was extracted with CH₂Cl₂ (40 mL) twotimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine16 (122 mg, 78%). ¹H NMR (400 MHz, CDCl₃): δ 8.55 (s, 1H, H-2), 7.79 (d,1H, J=9.2 Hz, Ph-H), 7.35 (s, 1H, H-8), 7.15 (d, 1H, J=3.2 Hz, Ph-H),6.68 (dd, 1H, J=3.2 and 9.2 Hz, Ph-H), 6.33 (dd, 1H, J=5.6 and 8.8 Hz,H-1′), 5.26 (s, 1H, Ph-CH), 4.85 (d, 1H, J=8.8 Hz, 7-CH₂a), 4.75 (m, 1H,H-3′), 4.70 (d, 1H, J=8.8 Hz, 7-CH₂b), 4.13 (m, 1H, H-4′), 3.95 (m, 1H,H-5′a), 3.83 (s, 3H, OCH₃), 3.78 (m, 1H, H-5′b), 2.86 (m, 1H, H-2′a),2.30 (m, 1H, H-2′b), 0.83 (s, 9H, C(CH₃)₃).

Compound 16 (120 mg, 0.23 mmol) was dissolved in 1,4-dioxane (10 mL)followed by addition of NH₃ in MeOH (7 N, 10 mL). The mixture wastransferred to a sealed tube and stirred at 100° C. for 24 hours, thencooled to room temperature, concentrated in vacuo, and the residue waspurified by silica gel chromatography to yield7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine17 (87 mg, 74%). ¹H NMR (400 MHz, DMSO-d₆): δ 8.06 (s, 1H, H-2), 7.97(d, 1H, J=9.2 Hz, Ph-H), 7.22 (s, 1H, H-8), 7.08 (d, 1H, J=2.8 Hz,Ph-H), 7.05 (dd, 1H, J=2.8 and 9.2 Hz, Ph-H), 6.66 (bs, 2H, D₂Oexchangeable, 6-NH₂), 6.42 (dd, 1H, J=6.0 and 8.0 Hz, H-1′), 5.25 (d,1H, D₂O exchangeable, 3′-OH), 5.15 (s, 1H, Ph-CH), 5.03 (t, 1H, D₂Oexchangeable, 5′-OH), 4.64 (d, 1H, J=12.8 Hz, 7-CH₂a), 4.43 (d, 1H,J=12.8 Hz, 7-CH₂b), 4.30 (m, 1H, H-3′), 3.84 (s, 3H, OCH₃), 3.77 (m, 1H,H-4′), 3.45 (m, 2H, H-5′), 2.43 (m, 1H, H-2′a), 2.14 (m, 1H, H-2′b),0.75 (s, 9H, C(CH₃)₃).

Compound 17 (21 mg, 0.042 mmol) was phosphorylated with POCl₃ (40 μL,0.43 mmol) and proton sponge (18 mg, 0.084 mmol) in trimethylphosphate(0.35 mL) at 0° C. for 7.5 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to yield7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine-5-′-triphosphatedA.VI, which was further purified using RP-HPLC. HRMS (ESI): For themolecular ion C₂₄H₃₃N₅O₁₆P₃ [M−H]⁻, the calculated mass was 740.1135,and the observed mass was 740.1156.

Example 4 Synthesis of 7-HOMe-7-Deaza-2′-deoxyguanosine TriphosphateAnalogs7-(2-nitrobenzyloxyl)methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

Compound 18 (Seela and Peng, 2005, which is incorporated by referenceherein) (1.35 g, 3.29 mmol) was evaporated from anhydrous pyridine (3.0mL) three times and then dissolved in anhydrous DMF (6.0 mL).tert-Butyldimethylsilyl chloride (5.95 g, 39.5 mmol) and imidazole (5.37g, 78.9 mmol) were added, and the mixture was stirred at 50° C. for 48hours with additional tert-butyldimethylsilyl chloride (2.97 g, 19.7mmol) and imidazole (2.69 g, 39.4 mmol) being added every six hours. Thereaction mixture was concentrated in vacuo and purified by silica gelchromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-2-(tert-butyldimethylsilyl)amino-6-chloro-7-iodo-7-deazapurine19 (1.48 g, 60% yield) as a white foam. ¹H NMR (400 MHz, CDCl₃): δ 7.35(s, 1H, H-8), 6.53 (t, 1H, J=6.0 Hz, H-1′), 4.70 (s, 1H, 2-NH), 4.47 (m,1H, H-3′), 3.97 (m, 1H, H-4′), 3.78 (m, 2H, H-5′a and H-5′b), 2.23 (m,2H, H-2′a and H-2′b), 0.98 (s, 9H, (CH₃)₃CSi), 0.95 (s, 9H, (CH₃)₃CSi),0.90 (s, 9H, (CH₃)₃CSi), 0.29 (2 s, 6H, (CH₃)₂Si), 0.13 (2 s, 6H,CH₃)₂Si), 0.09 (s, 6H, CH₃)₂Si).

A solution of compound 19 (720 mg, 0.96 mmol) was dissolved in anhydrous1,4-dioxane (30 mL). Anhydrous MeOH (30 mL) and triethylamine (0.58 mL)were added, and the mixture was stirred for 10 min under a COatmosphere, followed by addition ofbis(benzonitrile)dichloropalladium(II) (20 mg, 0.05 mmol). The reactionwas stirred at 58° C. for 24 hours under a CO atmosphere, and thenconcentrated in vacuo. The residue was purified by silica gelchromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-2-(tert-butyldimethylsilyl)amino-6-chloro-7-methoxycarbonyl-7-deazapurine20 (600 mg, 91%) as a viscous oil. ¹H NMR (400 MHz, CDCl₃): δ 7.92 (s,1H, H-8), 6.57 (dd, 1H, J=8.0 and 6.0 Hz, H-1′), 4.78 (s, 1H, 2-NH),4.49 (m, 1H, H-3′), 4.02 (m, 1H, H-4′), 3.85 (s, 3H, CH₃), 3.81 (m, 2H,H-5′a and H-5′b), 2.25 (m, 2H, H-2′a and H-2′b), 0.98 (s, 9H,(CH₃)₃CSi), 0.93 (s, 9H, (CH₃)₃CSi), 0.92 (s, 9H, (CH₃)₃CSi), 0.31 (s,6H, (CH₃)₂Si), 0.13 (2 s, 6H, (CH₃)₂Si), 0.11 (s, 6H, (CH₃)₂Si).

To a solution of compound 20 (1.11 g, 1.63 mmol) in anhydrous THF (56mL), lithium borohydride (143 mg, 6.5 mmol) was added, followed by MeOH(0.94 mL). The reaction mixture was heated to reflux for one hour. Uponcooling to room temperature, the reaction mixture was diluted withCH₂Cl₂ (700 mL) and quenched with water (70 mL). The organic phase wasseparated, dried over Na₂SO₄, and concentrated in vacuo. The residue waspurified by silica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-2-(tert-butyldimethylsilyl)amino-6-chloro-7-hydroxymethyl-7-deazapurine21 (0.58 g, 54%) as a viscous oil. ¹H NMR (400 MHz, CDCl₃): δ 7.16 (s,1H, H-8), 6.56 (t, 1H, J=6.4 Hz, H-1′), 4.79 (AB d, J=13.6 Hz, 7-CH₂a),4.75 (AB d, J=13.6 Hz, 7-CH₂b), 4.70 (s, 1H, 2-NH), 4.50 (m, 1H, H-3′),3.96 (m, 1H, H-4′), 3.76 (m, 2H, H-5′a and H-5′b), 2.23 (m, 2H, H-2′aand H-2′b), 0.98 (s, 9H, (CH₃)₃CSi), 0.94 (s, 9H, (CH₃)₃CSi), 0.92 (s,9H, (CH₃)₃CSi), 0.30 (s, 3H, (CH₃)₂Si), 0.29 (s, 3H, (CH₃)₂Si), 0.11 (s,6H, (CH₃)₂Si), 0.10 (s, 6H, (CH₃)₂Si).

To a solution of compound 21 (150 mg, 0.23 mmol) in CH₂Cl₂ (3.0 mL),n-Bu₄NBr (37 mg, 0.12 mmol), 2-nitrobenzyl bromide (148 mg, 0.68 mmol)and NaOH solution (1 M, 3.0 mL) were added. The reaction mixture wasstirred vigorously at room temperature for two days in the dark. Theorganic phase was separated, dried over Na₂SO₄, concentrated in vacuo,and purified by silica gel chromatography to yield9-[β-D-3′,5′-O-bis-(tert-butyldimethylsilyl)-2′-deoxyribofuranosyl]-2-(tert-butyldimethylsilyl)amino-6-chloro-7-(2-nitrobenzyloxyl)methyl-7-deazapurine22 (87 mg, 48%) as a viscous oil. ¹H NMR (400 MHz, CDCl₃): δ 8.06 (dd,1H, J=8.0 and 1.2 Hz, Ph-H), 7.87 (d, 1H, J=7.2 Hz, Ph-H), 7.61 (dt, 1H,J=7.6 and 1.2 Hz, Ph-H), 7.43 (m, 1H, Ph-H), 7.20 (s, 1H, H-8), 6.56(dd, 1H, J=7.6 and 6.0 Hz, H-1′), 4.99 (s, 2H, PhCH₂), 4.83 (AB d, 1H,J=11.4 Hz, 7-CH₂a), 4.75 (AB d, 1H, J=11.4 Hz, 7-CH₂b), 4.67 (s, 1H,2-NH), 4.50 (m, 1H, H-3′), 3.96 (m, 1H, H-4′), 3.77 (m, 2H, H-5′a andH-5′b), 2.25 (m, 2H, H-2′a and H-2′b), 0.98 (s, 9H, (CH₃)₃CSi), 0.92 (s,18H, (CH₃)₃CSi), 0.30 (s, 3H, (CH₃)₂Si), 0.29 (s, 3H, (CH₃)₂Si), 0.09(m, 12H, (CH₃)₂Si).

A solution of n-Bu₄NF (123 mg, 0.39 mmol) in THF (2.0 mL) was addeddropwise to a solution of compound 22 (105 mg, 0.13 mmol) in THF (3.0mL) at 0° C. The reaction mixture was stirred at 0° C. for one hour andthen at room temperature for two hours. The mixture was concentrated invacuo and purified by silica gel chromatography to yield2-amino-6-chloro-9-[β-D-2′-deoxy-ribofuranosyl]-7-(2-nitrobenzyloxyl)methyl-7-deazapurine23 (57 mg, 95%) as a yellow foam. ¹H NMR (400 MHz, DMSO-d6): δ, 8.02 (m,1H, Ph-H), 7.74 (m, 2H, Ph-H), 7.55 (m, 1H, Ph-H), 7.41 (s, 1H, H-8),6.73 (s, 2H, D₂O exchangeable, NH₂), 6.41 (dd, 1H, J=8.4 and 6.0 Hz,H-1′), 5.26 (d, 1H, D₂O exchangeable, 3′-OH), 4.91 (t, 1H, D₂Oexchangeable, 5′-OH), 4.88 (s, 2H, Ph-CH₂), 4.66 (dd, 2H, J=11.6 Hz,7-CH₂), 4.31 (m, 1H, H-3′), 3.78 (m, 1H, H-4′), 3.50 (m, 2H, H-5′), 2.38(m, 1H, H-2′a), 2.15 (m, 1H, H-2′b).

A mixture of 23 (38 mg, 0.085 mmol) and 1,4-diazabicyclo[2.2.2]octane(11 mg, 0.1 mmol) in water (4.0 mL) was heated to reflux for four hoursunder a nitrogen atmosphere. Water was removed in vacuo, and the residuewas evaporated from MeOH (3.0 mL) three times, and purified by silicagel chromatography to yield7-(2-nitrobenzyloxyl)methyl-7-deaza-2′-deoxyguanosine 24 (11 mg, 30%).¹H NMR (400 MHz, DMSO-d6): δ 10.4 (s, 1H, D₂O exchangeable, N—H), 8.03(dd, 1H, J=8.4 and 0.8 Hz, Ph-H), 7.83 (d, 1H, J=7.6 Hz, Ph-H), 7.73 (m,1H, Ph-H), 7.55 (m, 1H, Ph-H), 6.92 (s, 1H, H-8), 6.28 (m, 1H, H-1′),6.26 (bs, 2H, D₂O exchangeable, NH₂), 5.21 (d, 1H, D₂O exchangeable,3′-OH), 4.89 (t, 1H, D₂O exchangeable, 5′-OH), 4.88 (s, 2H, Ph-CH₂),4.60 (dd, 2H, 7-CH₂), 4.28 (m, 1H, H-3′), 3.74 (m, 1H, H-4′), 3.48 (m,2H, H-5′), 2.32 (m, 1H, H-2′a), 2.08 (m, 1H, H-2′b).

Compound 24 (11 mg, 0.025 mmol) was phosphorylated with POCl₃ (15 μL,0.05 mmol) and proton sponge (11 mg, 0.05 mmol) in trimethylphosphate(0.3 mL) at 0° C. for two hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (118 mg, 0.25 mmol) andtri-n-butylamine (50 μL) in anhydrous DMF (0.5 mL) was added. After 30min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 5.0mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in water (10mL), filtered, and purified by anion exchange chromatography. Thefractions containing triphosphate were combined and lyophilized to give7-(2-nitrobenzyloxyl)methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.I, which was further purified using RP-HPLC. HRMS (ESI): For themolecular ion C₁₉H₂₃N₅O₁₆P₃ [M−H]⁻, the calculated mass was 670.0353,and the observed mass was 670.0344.

7-[1-(2-Nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

DMAP (148 mg, 1.2 mmol) and MsCl (71 μL, 0.9 mmol) were added to asolution of compound 21 (200 mg, 0.30 mmol) in anhydrous CH₂Cl₂ (5.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 min and diluted with CH₂Cl₂ (15 mL). The solution was applied ona short silica gel plug (2×3 cm) and was eluted quickly withhexane/ethyl acetate/triethylamine solvent system (volume ratio:80/20/0.5). The eluent was concentrated in vacuo, and the residue wasmixed with racemic (R/S)-1-(2-nitrophenyl)-2,2-dimethyl-1-propanol (500mg, 2.4 mmol). The mixture was heated at 115° C. for 45 min under anitrogen atmosphere, cooled to room temperature and then dissolved inTHF (10 mL) followed by addition of n-Bu₄NF (283 mg, 0.90 mmol). Themixture was stirred at room temperature for four hours and thenconcentrated in vacuo. The residue was dissolved in CH₂Cl₂ (25 mL) andwashed with brine (25 mL), and the aqueous phase was extracted withCH₂Cl₂ (25 mL) two times. The combined organic phase was dried overNa₂SO₄, concentrated in vacuo, and the residue was purified by silicagel chromatography to yield2-amino-6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine25 (40 mg, 26% for three steps) as a 1:1 mixture of two diastereomers.

To a solution of compound 25 (40 mg, 0.08 mmol) in 1,4-dioxane (1.0 mL)and DMF (2.0 mL), syn-pyrimidine-2-aldoxime (180 mg, 1.5 mmol) and1,1,3,3-tetramethyl guanidine (211 μL, 1.68 mmol) were added. Themixture was heated at 70° C. overnight under a nitrogen atmosphere. Thereaction mixture was diluted with CH₂Cl₂ (20 mL) and washed sequentiallywith acetic acid solution (0.1 M, 30 mL), saturated NaHCO₃ solution (30mL), and brine (30 mL). The organic phase was dried over Na₂SO₄,concentrated in vacuo, and the residue was purified by silica gelchromatography to yield7-[1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine26 (27 mg, 70%) as a 1:1 mixture of two diastereomers. ¹H NMR (400 MHz,MeOH-d₄) for diastereomers: δ 7.79 (m, 1H, Ph-H), 7.73 (m, 1H, Ph-H),7.56 (m, 1H, Ph-H), 7.39 (m, 1H, Ph-H), 6.87 and 6.86 (2 s, 1H, H-8),6.30 (m, 1H, H-1′), 4.99 and 4.97 (2 s, 1H, Ph-CH), 4.63-4.36 (m, 3H,7-CH₂ and H-3′), 3.91 (m, 1H, H-4′), 3.69 (m, 2H, H-5′), 2.48 (m, 1H,H-2′a), 2.20 (m, 1H, H-2′b), 0.79 and 0.77 (2 s, 9H, (CH₃)₃).

Compound 26 (25 mg, 0.05 mmol) was phosphorylated with POCl₃ (20 μL,0.21 mmol) and proton sponge (21 mg, 0.1 mmol) in trimethylphosphate(0.35 mL) at 0° C. for 3.5 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give7-[1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.V.a as a 1:1 mixture of two diastereomers, which were separated usingRP-HPLC to yield the single diastereomers dG.V.a ds1 and dG.V.a ds2.HRMS (ESI): For the molecular ion C₂₃H₃₁N₅O₁₆P₃ [M−H]⁻, the calculatedmass was 726.0979, and the observed mass was 726.0992.

7-[(S)-1-(2-Nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

DMAP (224 mg, 1.8 mmol) and MsCl (107 μL, 1.4 mmol) were added to asolution of compound 21 (300 mg, 0.46 mmol) in anhydrous CH₂Cl₂ (10 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 min and diluted with CH₂Cl₂ (20 mL). The solution was applied ona short silica gel plug (2×3 cm) and was eluted quickly withhexane/ethyl acetate/triethylamine solvent system (volume ratio80/20/0.5). The eluent was concentrated in vacuo, and residue was mixedwith (S)-1-(2-nitrophenyl)-2,2-dimethyl-1-propanol (520 mg, 2.5 mmol).The mixture was heated at 115° C. for 45 min under a nitrogenatmosphere, cooled to room temperature and dissolved in THF (20 mL)followed by addition of n-Bu₄NF (491 mg, 1.6 mmol). The mixture wasstirred at room temperature for four hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (20 mL) and washed with brine(30 mL), and the aqueous phase was extracted with CH₂Cl₂ (20 mL) twotimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield2-amino-6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine27 (81 mg, 35% for three steps). ¹H NMR (400 MHz, MeOH-d₄): δ 7.79 (m,2H, Ph-H), 7.60 (dt, 1H, J=1.2 and 8.0 Hz, Ph-H), 7.46 (dt, 1H, J=1.2and 8.0 Hz, Ph-H), 7.27 (s, 1H, H-8), 6.47 (dd, 1H, J=6.4 and 8.0 Hz,H-1′), 4.98 (s, 1H, Ph-CH), 4.71 (d, 1H, J=12.4 Hz, 7-CH₂a), 4.50 (m,1H, H-3′), 4.47 (d, 1H, J=12.4 Hz, 7-CH₂b), 3.96 (m, 1H, H-4′), 3.73 (m,2H, H-5′), 2.59 (m, 1H, H-2′a), 2.30 (m, 1H, H-2′b), 0.80 (s, 9H,(CH₃)₃).

Compound 27 (104 mg, 0.21 mmol) was dissolved in a solution of sodiummethoxide in MeOH (0.5 M, 10 mL), and the mixture was heated to refluxfor one hour under a nitrogen atmosphere. The reaction mixture wascooled to room temperature, neutralized with acetic acid, and thenconcentrated in vacuo. The residue was purified by silica gelchromatography to yield2-amino-6-methoxy-9-[β-D-2′-deoxyribofuranosyl]-7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine28 (75 mg, 74%). ¹H NMR (400 MHz, CDCl₃): δ 7.74 (m, 2H, Ph-H), 7.52 (t,1H, J=8.0 Hz, Ph-H), 7.36 (t, 1H, J=8.0 Hz, Ph-H), 6.71 (s, 1H, H-8),6.47 (dd, 1H, J=5.6 and 9.6 Hz, H-1′), 5.04 (s, 1H, Ph-CH), 4.71 (m, 1H,H-3′), 4.47 (dd, 2H, J=12Hz, 7-CH₂), 4.15 (m, 1H, H-4′), 3.94 (s, 3H,OCH₃), 3.76 (m, 2H, H-5′), 3.01 (m, 1H, H-2′a), 2.19 (m, 1H, H-2′b),0.82 (s, 9H, (CH₃)₃).

Compound 28 (70 mg, 0.14 mmol) was dissolved in 1,4-dioxane (6.0 mL)followed by addition of an aqueous solution of sodium hydroxide (2 M, 12mL). The mixture was heated to reflux for four days under a nitrogenatmosphere, cooled to room temperature, neutralized with dilutehydrochloric acid (1 M), and concentrated in vacuo. The residue wasevaporated from MeOH (5.0 mL) three times and then purified by silicagel chromatography to yield7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine29 (22 mg, 33%). Starting material 28 (42 mg, 60%) was also recoveredfrom the reaction. ¹H NMR (400 MHz, CDCl₃): δ 11.02 (br s, 1H, NH), 7.69(m, 2H, Ph-H), 7.52 (t, 1H, J=7.2 Hz, Ph-H), 7.33 (t, 1H, J=7.2 Hz,Ph-H), 6.66 (s, 1H, H-8), 6.13 (t, 1H, J=6.8 Hz, H-1′), 6.03 (br s, 2H,6-NH₂), 4.92 (s, 1H, Ph-CH), 4.77 (m, 1H, H-3′), 4.57 (d, 1H, J=12.8 Hz,7-CH₂a), 4.12 (m, 1H, H-4′), 3.05 (d, 1H, J=12.8 Hz, 7-CH₂ b), 3.75 (m,2H, H-5′), 2.87 (m, 1H, H-2′a), 2.29 (m, 1H, H-2′b), 0.76 (s, 9H,(CH₃)₃).

Compound 29 (16 mg, 0.033 mmol) was phosphorylated with POCl₃ (17 μL,0.18 mmol) and proton sponge (14 mg, 0.066 mmol) in trimethylphosphate(0.35 mL) at 0° C. for four hours under a nitrogen atmosphere. Asolution of bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol)and tri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After10 min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5;10 mL) was added. The reaction was stirred at room temperature for onehour and then concentrated in vacuo. The residue was dissolved in 20%aqueous acetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give7-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.V, which was further purified using RP-HPLC conditions. The retentiontime of dG.V was identical to that of dG.V.a ds2 by RP-HPLC analysisusing the same condition (data not shown). HRMS (ESI): For the molecularion C₂₃H₃₁N₅O₁₆P₃ [M−H]⁻, the calculated mass was 726.0979, and theobserved mass was 726.0986.

7-[1-(4-Methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

DMAP (346 mg, 2.8 mmol) and MsCl (165 μL, 2.1 mmol) were added to asolution of compound 21 (470 mg, 0.72 mmol) in anhydrous CH₂Cl₂ (5.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 min and diluted with CH₂Cl₂ (20 mL). The solution was applied ona short silica gel plug (2×3 cm) and was eluted quickly withhexane/ethyl acetate/triethylamine solvent system (volume ratio80/20/0.5). The eluent was concentrated in vacuo, and the residue wasmixed with racemic(R/S)-1-(4-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (1.6 g, 6.69mmol). The mixture was heated to 115° C. for 45 min under a nitrogenatmosphere, cooled to room temperature, and dissolved in THF (20 mL)followed by addition of n-Bu₄NF (788 mg, 2.5 mmol). The mixture wasstirred at room temperature for four hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (20 mL) and washed with brine(30 mL), and the aqueous phase was extracted with CH₂Cl₂ (20 mL) twotimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield2-amino-6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[(S)-1-(4-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]-methyl-7-deazapurine30 (80 mg, 21% for three steps) as a 1:1 mixture of two diastereomers.

To a solution of compound 30 (80 mg, 0.15 mmol) in 1,4-dioxane (1.0 mL)and DMF (2.0 mL), syn-pyrimidine-2-aldoxime (366 mg, 3.0 mmol) and1,1,3,3-tetramethyl guanidine (414 μL, 3.3 mmol) were added, and themixture was heated at 70° C. overnight under a nitrogen atmosphere. Thereaction mixture was diluted with CH₂Cl₂ (20 mL) and washed sequentiallywith acetic acid (0.1 M, 30 mL), saturated NaHCO₃ solution (30 mL), andbrine (30 mL). The organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield7-[(S)-1-(4-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxy-guanosine31 (45 mg, 59%) as a 1:1 mixture of two diastereomers. ¹H NMR (400 MHz,DMSO-d₆) for diastereomers: δ 10.31 (br s, 1H, D₂O exchangeable, NH),7.63 and 7.62 (2 d, 1H, J=2.8 Hz, Ph-H), 7.41 and 7.40 (2 d, 1H, J=2.8Hz, Ph-H), 7.27 (m, 1H, Ph-H), 6.98 and 6.96 (2 s, 1H, H-8), 6.28 (m,1H, H-1′), 6.22 (br s, 2H, D₂O exchangeable, NH₂), 5.22 (d, 1H, D₂Oexchangeable, 3′-OH), 4.88 (t, 1H, D₂O exchangeable, 5′-OH), 4.73 and4.71 (2 s, 1H, Ph-CH), 4.47-4.24 (m, 3H, 7-CH₂ and H-3′), 3.85 and 3.83(2 s, 3H, OCH₃), 3.74 (m, 1H, H-4′), 3.48 (m, 2H, H-5′), 2.28 (m, 1H,H-2′a), 2.06 (m, 1H, H-2′b), 0.80 and 0.78 (2 s, 9H, (CH₃)₃).

Compound 31 (25 mg, 0.048 mmol) was phosphorylated with POCl₃ (15 μL,0.18 mmol) and proton sponge (21 mg, 0.10 mmol) in trimethylphosphate(0.35 mL) at 0° C. for 3.5 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give7-[1-(4-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.V.b as a 1:1 mixture of two diastereomers, which were separated usingRP-HPLC to yield the single diastereomers dG.V.b ds1 and dG.V.b ds2.HRMS (ESI): For the molecular ion C₂₄H₃₃N₅O₁₇P₃ [M−H]⁻, the calculatedmass was 756.1084, and the observed mass was 756.1101.

7-[1-(5-Methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

DMAP (302 mg, 2.5 mmol) and MsCl (145 μL, 1.9 mmol) were added to asolution of compound 21 (410 mg, 0.62 mmol) in anhydrous CH₂Cl₂ (5.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 min and diluted with CH₂Cl₂ (20 mL). The solution was applied ona short silica gel plug (2×3 cm) and was eluted quickly with ahexane/ethyl acetate/triethylamine solvent system (volume ratio:80/20/0.5). The eluent was concentrated in vacuo, and residue was mixedwith racemic (R/S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol(800 mg, 2.2 mmol). The mixture was heated at 115° C. for 45 min under anitrogen atmosphere, cooled to room temperature, and dissolved in THF(10 mL) followed by addition of n-Bu₄NF (683 mg, 3.3 mmol). The mixturewas stirred at room temperature for four hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (20 mL) and washed with brine(30 mL), and the aqueous phase was extracted with CH₂Cl₂ (20 mL) twotimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield2-amino-6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine32 (80 mg, 24% for three steps) as a 1:1 mixture of two diastereomers.¹H NMR (400 MHz, CDCl₃) for diastereomers: δ 7.86 and 7.83 (2 d, 1H,J=8.8 Hz, Ph-H), 7.19 and 7.17 (2 d, 1H, J=2.8 Hz, Ph-H), 6.91 and 6.90(2 s, 1H, H-8), 6.80 and 6.75 (2 dd, 1H, J=0.8 and 8.8 Hz, Ph-H), 6.17(m, 1H, H-1′), 5.23 and 5.21 (2 s, 1H, Ph-CH), 5.01 and 5.00 (2 br s,2H, NH₂), 4.73 (m, 1H, H-3′), 4.65-4.49 (m, 2H, 7-CH₂), 4.14 (m, 1H,H-4′), 3.84 (m, 5H, H-5′ and OCH₃), 2.78 (m, 1H, H-2′a), 2.33 (m, 1H,H-2′b), 0.82 and 0.81 (2 s, 9H, (CH₃)₃).

To a solution of compound 32 (80 mg, 0.15 mmol) in 1,4-dioxane (1.0 mL)and DMF (2.0 mL), syn-pyrimidine-2-aldoxime (360 mg, 3.0 mmol) and1,1,3,3-tetramethyl guanidine (414 μL, 3.3 mmol) were added, and themixture was heated at 70° C. overnight under a nitrogen atmosphere. Thereaction mixture was diluted with CH₂Cl₂ (20 mL) and washed sequentiallywith acetic acid (0.1 M, 30 mL), saturated NaHCO₃ solution (30 mL), andbrine (30 mL). The organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield7-[1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine33 (43 mg, 57%) as a 1:1 mixture of two diastereomers. ¹H NMR (400 MHz,DMSO-d₆) for diastereomers: δ 10.34 (br s, 1H, D₂O exchangeable, NH),7.92 and 7.89 (2 d, 1H, J=8.8 Hz, Ph-H), 7.15 (m, 1H, Ph-H), 6.95 (m,1H, Ph-H), 6.82 and 6.81 (2 s, 1H, H-8), 6.22 (m, 3H, 2H D₂Oexchangeable, H-1′ and NH₂), 5.19 (d, 1H, D₂O exchangeable, 3′-OH), 5.12and 5.10 (2 s, 1H, Ph-CH), 4.84 (t, 1H, D₂O exchangeable, 5′-OH),4.47-4.31 (m, 2H, 7-CH₂), 4.24 (m, 1H, H-3′), 3.85 and 3.83 (2 s, 3H,OCH₃), 3.71 (m, 1H, H-4′), 3.44 (m, 2H, H-5′), 2.24 (m, 1H, H-2′a), 2.01(m, 1H, H-2′b), 0.76 and 0.74 (2 s, 9H, (CH₃)₃).

Compound 33 (20 mg, 0.04 mmol) was phosphorylated with POCl₃ (25 μL,0.27 mmol) and proton sponge (16 mg, 0.08 mmol) in trimethylphosphate(0.30 mL) at 0° C. for six hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give7-[1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.V.c as a 1:1 mixture of two diastereomers, which were separated usingRP-HPLC to yield the single diastereomers dG.V.c ds1 and dG.V.c ds2.HRMS (ESI): For the molecular ion C₂₄H₃₃N₅O₁₇P₃ [M−H]⁻, the calculatedmass was 756.1084, and the observed mass was 756.1088.

7-[1-(4,5-Dimethoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

DMAP (273 mg, 2.2 mmol) and MsCl (130 μL, 1.7 mmol) were added to asolution of compound 21 (370 mg, 0.56 mmol) in anhydrous CH₂Cl₂ (5.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 30 min and diluted with CH₂Cl₂ (25 mL). The solution was applied ona short silica gel plug (2×3 cm) and was eluted quickly with ahexane/ethyl acetate/triethylamine solvent system (volume ratio:80/20/0.5). The eluent was concentrated in vacuo, and the residue wasmixed with racemic(R/S)-1-(4,5-dimethoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (800 mg,3.0 mmol). The mixture was heated at 115° C. for 45 min under a nitrogenatmosphere, cooled to room temperature and dissolved in THF (10 mL)followed by addition of n-Bu₄NF (530 mg, 1.7 mmol). The mixture wasstirred at room temperature for two hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (40 mL) and washed with brine(50 mL), and the aqueous phase was extracted with CH₂Cl₂ (40 mL) twotimes. The combined organic phase was dried over Na₂SO₄ and concentratedin vacuo, and the residue was purified by silica gel chromatography toyield2-amino-6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[1-(4,5-dimethoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deazapurine34 (70 mg, 23% for three steps) as a 1:1 mixture of two diastereomers.¹H NMR (400 MHz, CDCl₃) for diastereomers: δ 7.42 and 7.39 (2 s, 1H,Ph-H), 7.15 and 7.13 (2 s, 1H, Ph-H), 6.89 and 6.84 (2 s, 1H, H-8), 6.12(m, 1H, H-1′), 5.22 and 5.16 (2 s, 1H, Ph-CH), 5.10 and 5.08 (2 bs, 2H,NH₂), 4.71-4.41 (m, 3H, H-3′ and 7-CH₂), 4.13 (m, 1H, H-4′), 3.94 (4 s,7H, OCH₃×2 and H-5′a), 3.78 (m, 1H, H-5′b), 2.90 (m, 1H, H-2′a), 2.25(m, 1H, H-2′b), 0.82 and 0.80 (2 s, 9H, (CH₃)₃).

To a solution of compound 34 (65 mg, 0.11 mmol) in 1,4-dioxane (1.0 mL)and DMF (2.0 mL), syn-pyrimidine-2-aldoxime (292 mg, 2.4 mmol) and1,1,3,3-tetramethyl guanidine (330 μL, 2.6 mmol) were added, and themixture was heated at 70° C. overnight under a nitrogen atmosphere. Thereaction mixture was diluted with CH₂Cl₂ (40 mL) and washed sequentiallywith acetic acid (0.1 M, 50 mL), saturated NaHCO₃ solution (50 mL), andbrine (50 mL). The organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield7-[1-(4,5-dimethoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine35 (42 mg, 68%) as a 1:1 mixture of two diastereomers. ¹H NMR (400 MHz,DMSO-d₆) for diastereomers: δ 10.33 (br s, 1H, D₂O exchangeable, NH),7.47 and 7.44 (2 s, 1H, Ph-H), 7.16 and 7.15 (2 s, 1H, Ph-H), 6.83 and6.82 (2 s, 1H, H-8), 6.22 (m, 3H, 2H D₂O exchangeable, NH₂ and H-1′),5.18 (br s, 1H, D₂O exchangeable, 3′-OH), 5.06 and 5.04 (2 s, 1H,Ph-CH), 4.83 (t, 1H, D₂O exchangeable, 5′-OH), 4.44-4.23 (m, 3H, 7-CH₂and H-3′), 3.82 (4 s, 6H, OCH₃×2), 3.70 (m, 1H, H-4′), 3.42 (m, 2H,H-5′), 2.22 (m, 1H, H-2′a), 2.01 (m, 1H, H-2′b), 0.77 and 0.75 (2 s, 9H,(CH₃)₃).

Compound 35 (40 mg, 0.073 mmol) was phosphorylated with POCl₃ (14 μL,0.15 mmol) and proton sponge (31 mg, 0.15 mmol) in trimethylphosphate(0.35 mL) at 0° C. for two hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give7-[1-(4,5-dimethoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.V.d as a 1:1 mixture of two diastereomers, which were separated usingRP-HPLC to yield the single diastereomers dG.V.d ds1 and dG.V.d ds2.HRMS (ESI): For the molecular ion C₂₅H₃₅N₅O₁₈P₃ [M−H]⁻, the calculatedmass was 786.1190, and the observed mass was 786.1206.

7-[(S)-1-(5-Methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate

DMAP (224 mg, 1.8 mmol) and MsCl (106 μL, 1.4 mmol) were added to asolution of compound 21 (300 mg, 0.46 mmol) in anhydrous CH₂Cl₂ (5.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 min and diluted with CH₂Cl₂ (20 mL). The solution was applied ona short silica gel plug (2×3 cm) and was eluted quickly with ahexane/ethyl acetate/triethylamine solvent system (volume ratio:80/20/0.5). The eluent was concentrated in vacuo, and residue was mixedwith (S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (500 mg,2.1 mmol). The mixture was heated at 115° C. for 45 min under a nitrogenatmosphere, cooled to room temperature and dissolved in THF (10 mL)followed by addition of n-Bu₄NF (507 mg, 1.6 mmol). The mixture wasstirred at room temperature for four hours and then concentrated invacuo. The residue was dissolved in CH₂Cl₂ (20 mL) and washed with brine(30 mL), and the aqueous phase was extracted with CH₂Cl₂ (20 mL) twotimes. The combined organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield2-amino-6-chloro-9-[β-D-2′-deoxyribofuranosyl]-7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]-methyl-7deazapurine 36 (67 mg, 27% for three steps). ¹H NMR (400 MHz, CDCl₃): δ7.82 (d, 1H, J=8.8 Hz, Ph-H), 7.16 (d, 1H, J=2.8 Hz, Ph-H), 6.90 (s, 1H,H-8), 6.72 (dd, 1H, J=8.8 and 2.8 Hz, Ph-H), 6.12 (dd, 1H, J=9.2 and 6.0Hz, H-1′), 5.22 (s, 1H, Ph-CH), 5.15 (br s, 2H, NH₂), 4.69-4.55 (m, 3H,H-3′ and 7-CH₂), 4.11 (m, 1H, H-4′), 3.92 (m, 1H, H-5′a), 3.82 (s, 3H,OCH₃), 3.73 (m, 1H, H-5′b), 2.81 (m, 1H, H-2′a), 2.21 (m, 1H, H-2′b),0.82 (s, 9H, (CH₃)₃).

To a solution of compound 36 (65 mg, 0.12 mmol) in 1,4-dioxane (1.0 mL)and DMF (2.0 mL), syn-pyrimidine-2-aldoxime (292 mg, 2.4 mmol) and1,1,3,3-tetramethyl guanidine (331 μL, 2.6 mmol) were added, and themixture was heated at 70° C. overnight under a nitrogen atmosphere. Thereaction mixture was diluted with CH₂Cl₂ (20 mL) and washed sequentiallywith acetic acid (0.1 M, 30 mL), saturated NaHCO₃ solution (30 mL), andbrine (30 mL). The organic phase was dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine37 (48 mg, 76%). ¹H NMR (400 MHz, DMSO-d₆): δ 10.37 (br s, 1H, D₂Oexchangeable, NH), 7.95 (d, 1H, J=9.2 Hz, Ph-H), 7.18 (d, 1H, J=2.8 Hz,Ph-H), 7.03 (dd, 1H, J=9.2 and 2.8 Hz, Ph-H), 6.84 (s, 1H, H-8), 6.23(m, 3H, 2H D₂O exchangeable, NH₂ and H-1′), 5.20 (d, 1H, D₂Oexchangeable, 3′-OH), 5.13 (s, 1H, Ph-CH), 4.84 (t, 1H, D₂Oexchangeable, 5′-OH), 4.48 (d, 1H, J=12.0 Hz, 7-CH₂a), 4.32 (d, 1H,J=12.0 Hz, 7-CH₂b), 4.27 (m, 1H, H-3′), 3.88 (s, 3H, OCH₃), 3.73 (m, 1H,H-4′), 3.46 (m, 2H, H-5′), 2.30 (m, 1H, H-2′a), 2.05 (m, 1H, H-2′b),0.77 (s, 9H, (CH₃)₃).

Compound 37 (10 mg, 0.02 mmol) was phosphorylated with POCl₃ (26 μL,0.26 mmol) and proton sponge (8 mg, 0.04 mmol) in trimethylphosphate(0.3 mL) at 0° C. for 6.5 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (10 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give7-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine-5′-triphosphatedG.VI, which was further purified using RP-HPLC. The retention time ofdG.VI was identical to that of dG.V.c ds2 by RP-HPLC analysis under thesame condition. HRMS (ESI): For the molecular ion C₂₄H₃₃N₅O₁₇P₃ [M−H]⁻,the calculated mass was 756.1084, and the observed mass was 756.1101.

Example 5 Synthesis of 5-HOMe-2′-Deoxyuridine Triphosphate Analog5-[(S)-1-(5-Methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine-5′-triphosphate

Compound 38 (Litosh et al., 2011, which is incorporated herein byreference) (315 mg, 0.49 mmol) and(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (490 mg, 2.1mmol) were heated at 110° C. for 45 min under a nitrogen atmosphere. Themixture was cooled down to room temperature, dissolved in MeOH (10 mL),and followed by addition of NH₄F (400 mg, 11 mmol). The mixture wasstirred at 50° C. for 12 hours, concentrated in vacuo, dissolved inCH₂Cl₂ (50 mL), and washed with brine (50 mL). The organic phase wasdried over Na₂SO₄, concentrated in vacuo, and the residue was purifiedby silica gel chromatography to yield5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine39 (130 mg, 56%). ¹H NMR (400 MHz, CDCl₃): δ 9.14 (br s, 1H, NH), 7.90(d, 1H, J=9.2 Hz, Ph-H), 7.67 (s, 1H, H-6), 7.17 (d, 1H, J=2.8 Hz,Ph-H), 6.84 (dd, 1H, J=9.2 and 2.8 Hz, Ph-H), 6.18 (t, 1H, J=6.4 Hz,H-1′), 5.22 (s, 1H, Ph-CH), 4.56 (m, 1H, H-3′), 4.24 (d, 1H, J=12.4 Hz,5-CH₂a), 4.15 (d, 1H, J=12.4 Hz, 5-CH₂b), 4.00 (m, 1H, H-4′), 3.90 (m,1H, H-5′a), 3.88 (s, 3H, OCH₃), 3.81 (m, 1H, H-5′b), 2.35 (m, 2H, H-2),0.83 (s, 9H, C(CH₃)₃).

Compound 39 (30 mg, 0.065 mmol) was phosphorylated with POCl₃ (9 μL,0.097 mmol) and proton sponge (28 mg, 0.13 mmol) in trimethylphosphate(0.35 mL) at 0° C. for one hour under a nitrogen atmosphere. A solutionof tri-n-butylammonium pyrophosphate (147 mg, 0.32 mmol) andtri-n-butylamine (64 μL) in anhydrous DMF (0.64 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (10 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to yield5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine-5′-triphosphatedU.VI, which was further purified using RP-HPLC. HRMS (ESI): For themolecular ion C₂₂H₃₁N₃O₁₈P₃ [M−H]⁻, the calculated mass was 718.0815,and the observed mass was 718.0824.

Example 6 Synthesis of 5-HOMe-2′-Deoxycytidine Triphosphate Analogs5-(2-nitrobenzyloxyl)methyl-2′-deoxycytidine-5′-triphosphate

Compound 38 (300 mg, 0.46 mmol) and 2-nitrobenzyl alcohol (500 mg, 3.3mmol) were heated at 110° C. for 45 min under a nitrogen atmosphere. Themixture was cooled to room temperature, dissolved in THF (20 mL)followed by addition of n-Bu₄NF (362 mg, 1.2 mmol). The mixture wasstirred at room temperature for four hours, concentrated in vacuo, andthe residue was purified by silica gel chromatography to yield5-(2-nitrobenzyloxyl)methyl-2′-deoxyuridine 40 (Litosh et al., 2011,which is incorporated herein by reference) (95 mg, 53%). ¹H NMR (400MHz, CDCl₃): δ 8.45 (br s, 1H, NH), 8.05 (s, 1H, H-6), 8.02 (d, J=8.0Hz, 1H, Ph-H), 7.80 (d, 1H, J=8.0 Hz, Ph-H), 7.69 (t, 1H, J=8.0 Hz,Ph-H), 7.43 (t, 1H, J=8.0 Hz, Ph-H), 6.21 (t, 1H, J=6.0 Hz, H-1′), 4.94(dd, J=14.4 Hz, 2H, Ph-CH₂), 4.66 (m, 1H, H-3′), 4.35 (s, 2H, 5-CH₂),3.95 (m, 3H, H-4′ and H-5′), 2.42 (m, 1H, H-2′a), 2.30 (m, 1H, H-2′b).

To a solution of compound 40 (Litosh et al., 2011, which is incorporatedherein by reference) (70 mg, 0.18 mmol) in anhydrous DMF (2.0 mL), TBSCl(60 mg, 0.40 mmol) and imidazole (54 mg, 0.80 mmol) were added. Themixture was stirred at room temperature overnight under a nitrogenatmosphere, concentrated in vacuo, dissolved in CH₂Cl₂ (20 mL), andwashed with saturated NaHCO₃ solution (30 mL). The organic and aqueousphases were separated, and the aqueous phase was extracted with CH₂Cl₂(20 mL) two times. The combined organic phase was dried with Na₂SO₄,concentrated in vacuo, and the residue was purified by silica gelchromatography to yield3′,5′-O-bis-(tert-butyldimethylsilyl)-5-(2-nitrobenzyloxy)-methyl-2′-deoxyuridine41 (90 mg, 80%). ¹H NMR (400 MHz, CDCl₃): δ 8.04 (d, J=8.0 Hz, 1H,Ph-H), 7.98 (br s, 1H, NH), 7.80 (d, 1H, J=8.0 Hz, Ph-H), 7.74 (s, 1H,H-6), 7.64 (q, 1H, J=8.0 Hz, Ph-H), 7.44 (t, 1H, J=8.0 Hz, Ph-H), 6.21(q, 1H, J=6.0 Hz, H-1′), 4.95 (s, 2H, Ph-CH₂), 4.41 (m, 1H, H-3′), 4.34(dd, 2H, J=11.6 Hz, 5-CH₂), 3.96 (m, 1H, H-4′), 3.79 (m, 2H, H-5′), 2.29(m, 1H, H-2′a), 2.05 (m, 1H, H-2′b), 0.89 (2 s, 18H, C(CH₃)₃), 0.08 (4s, 12H, CH₃).

2,4,6-Triisopropyl benzenesulfonyl chloride (176 mg, 0.59 mmol) wasadded to a solution of compound 41 (85 mg, 0.14 mmol), DMAP (19 mg, 0.16mmol), and triethylamine (0.18 mL, 1.3 mmol) in anhydrous CH₂Cl₂ (5.0mL). The mixture was stirred at room temperature overnight under anitrogen atmosphere, concentrated in vacuo, and the residue wasdissolved in a solution of NH₃ in 1,4-dioxane (0.5 M, 15 mL). Themixture was transferred into a sealed tube and was heated at 90° C.overnight. The mixture was cooled to room temperature, concentrated invacuo, dissolved in CH₂Cl₂ (30 mL), and washed with brine (30 mL). Theorganic and aqueous phases were separated, and the aqueous phase wasextracted with CH₂Cl₂ (30 mL) two times. The combined organic phase wasdried over Na₂SO₄, concentrated in vacuo, and the residue was purifiedby silica gel column chromatography to yield3′,5′-O-bis-(tert-butyldimethylsilyl)-5-(2-nitrobenzyloxyl)methyl-2′-deoxycytidine42 (60 mg, 69% for two steps). ¹H NMR (400 MHz, CDCl₃): δ 8.08 (d, J=8.0Hz, 1H, Ph-H), 7.81 (s, 1H, H-6), 7.65 (m, 2H, Ph-H), 7.64 (q, 1H, J=8.0Hz, Ph-H), 7.49 (m, 1H, Ph-H), 6.29 (t, 1H, J=6.4 Hz, H-1′), 5.75 (br s,1H, NH₂), 4.85 (dd, 2H, J=13.6 Hz, Ph-CH₂), 4.41 (s, 2H, 5-CH₂), 4.34(m, 1H, H-3′), 3.95 (m, 1H, H-4′), 3.89 (dd, 1H, J=2.8 Hz, H-5′a), 3.76(dd, 1H, J=2.8 Hz, H-5′b), 2.46 (m, 1H, H-2′a), 1.98 (m, 1H, H-2′b),0.92 and 0.89 (2 s, 18H, C(CH₃)₃), 0.11-0.08 (4 s, 12H, CH₃).

To a solution of compound 42 (55 mg, 0.09 mmol) in THF (10 mL), n-Bu₄NF(63 mg, 0.20 mmol) was added. The mixture was stirred at roomtemperature for four hours and concentrated in vacuo, and the residuewas purified by silica gel column chromatography to yield5-(2-nitrobenzyloxyl)methyl-2′-deoxycytidine 43 (34 mg, 96%). ¹H NMR(400 MHz, DMSO-d₆): δ 8.05 (d, J=8.0 Hz, 1H, Ph-H), 7.89 (s, 1H, H-6),7.74 (m, 2H, Ph-H), 7.55 (m, 1H, Ph-H), 7.39 (br s, 1H, D₂Oexchangeable, NH₂), 6.74 (br s, 1H, D₂O exchangeable, NH₂), 6.12 (t, 1H,J=6.4 Hz, H-1′), 5.21 (br s, 1H, D₂O exchangeable, 3′-OH), 4.99 (br s,1H, D₂O exchangeable, 5′-OH), 4.81 (s, 2H, Ph-CH₂), 4.30 (dd, 2H, J=11.6Hz, 5-CH₂), 4.20 (m, 1H, H-3′), 3.76 (m, 1H, H-4′), 3.55 (m, 2H, H-5′),2.11 (m, 1H, H-2′a), 1.95 (m, 1H, H-2′b).

Compound 43 (32 mg, 0.081 mmol) was phosphorylated with POCl₃ (30 μL,0.32 mmol) and proton sponge (35 mg, 0.16 mmol) in trimethylphosphate(0.35 mL) at 0° C. for three hours under a nitrogen atmosphere. Asolution of tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give5-(2-nitrobenzyloxyl)methyl-2′-deoxycytidine-5′-triphosphate dC.I, whichwas further purified using RP-HPLC. HRMS (ESI): For the molecular ionC₁₇H₂₂N₄O₁₆P₃ [M−H]⁻, the calculated mass was 631.0244, and the observedmass was 631.0258.

5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine-5′-triphosphate

Compound 38 (Litosh et al., 2011, which is incorporated herein byreference) (520 mg, 0.80 mmol) and(S)-1-(2-nitrophenyl)-2,2-dimethyl-1-propanol (580 mg, 2.8 mmol) wereheated at 110° C. for one hour under a nitrogen atmosphere. The mixturewas cooled down to room temperature, dissolved in a minimum amount ofethyl acetate, and purified by silica gel chromatography to yield3′,5′-O-bis-(tert-butylsimethylsilyl)-5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine44 (115 mg, 21%). (3′ or5′)-O-(tert-butylsimethylsilyl)-5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine(78 mg, 17%) and5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine(16 mg, 4%) was also obtained from the reaction. ¹H NMR (400 MHz,CDCl₃): δ 8.97 (s, 1H, NH), 7.76 (d, 2H, J=8.0 Hz, Ph-H), 7.60 (m, 2H,Ph-H and H-6), 7.41 (s, 1H, Ph-H), 6.29 (dd, 1H, J=6.0 and 7.6 Hz,H-1′), 4.97 (s 1H, Ph-CH), 4.42 (m, 1H, H-3′), 4.28 (AB d, 1H, J=12.0Hz, 5-CH₂a), 4.06 (AB d, 1H, J=12.0 Hz, 5-CH₂b), 3.92 (m, 1H, H-4′),3.76 (m, 2H, H-5′), 2.30 (m, 1H, H-2′a), 2.05 (m, 1H, H-2′b), 0.95 (s,9H, (CH₃)₃CSi), 0.90 (s, 9H, (CH₃)₃CSi), 0.83 (s, 9H, (CH₃)₃C), 0.12 (s,3H, CH₃Si), 0.09 (s, 3H, CH₃Si), 0.07 (s, 3H, CH₃Si), 0.06 (s, 3H,CH₃Si). 2,4,6-Triisopropyl benzenesulfonyl chloride (61 mg, 0.20 mmol)was added to a solution of compound 44 (110 mg, 0.16 mmol), DMAP (20 mg,0.17 mmol), and triethylamine (63 μL, 0.45 mmol) in anhydrous CH₂Cl₂(3.0 mL). The mixture was stirred at room temperature for 36 hours undera nitrogen atmosphere, concentrated in vacuo, and the residue waspurified by silica gel column chromatography to give3′,5′-O-bis-(tert-butylsimethylsilyl)-5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-O⁴-(2,4,6-triisopropylbenzenesulfonyl)-2′-deoxyuridine45 (47 mg, 31%). ¹H NMR (500 MHz, CDCl₃): δ 8.08 (s, 1H, H-6), 7.80 (dd,1H, J=1.2 and 8.0 Hz, Ph-H), 7.78 (dd, 1H, J=1.6 and 8.0 Hz, Ph-H), 7.67(m, 1H, Ph-H), 7.46 (m, 1H, Ph-H), 7.20 (s, 2H, Ph-H), 6.09 (t, 1H,J=6.4 Hz, H-1′), 4.98 (s, 1H, Ph-CH), 4.35 (m, 1H, H-3′), 4.25 (AB d,1H, J=11.6 Hz, 5-CH₂a), 4.11 (AB d, 1H, J=11.6 Hz, 5-CH₂b), 3.97 (m, 1H,H-4′), 3.79 (dd, 1H, J=3.6 and 11.6 Hz, H-5′a), 3.74 (dd, 1H, J=11.6 and3.6 Hz, H-5′b), 2.90 (m, 1H, CH), 2.50 (m, 2H, H-2′), 1.98 (m, 2H, CH),1.31-1.22 (m, 18H, (CH₃)₂CH×3), 0.88 (2 s, 18H, (CH₃)₃CSi×2), 0.87 (s,9H, (CH₃)₃C), 0.07 (s, 6H, (CH₃)₂Si), 0.06 (s, 6H, (CH₃)₂Si).

A solution of NH₃ in 1,4-dioxane (0.5 M, 2.0 mL) was added to a solutionof compound 45 (47 mg, 0.05 mmol) in anhydrous 1,4-dioxane (2.0 mL). Themixture was transferred into a sealed tube and was heated at 90° C. forten hours. The mixture was cooled to room temperature, concentrated invacuo and the residue was purified by silica gel column chromatographyto yield3′,5′-O-bis-(tert-butyldimethylsilyl)-5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]-methyl-2′-deoxycytidine46 (31 mg, 91%). ¹H NMR (400 MHz, CDCl₃): δ 7.67 (m, 3H, Ph-H), 7.53 (s,1H, H-6), 7.45 (m, 1H, Ph-H), 6.30 (t, 1H, J=6.6 Hz, H-1′), 5.72 (br s,2H, NH₂), 4.88 (s, 1H, Ph-CH), 4.32 (m, 1H, H-3′), 4.28 (AB d, 1H,J=12.8 Hz, 5-CH₂a), 4.08 (AB d, 1H, J=12.8 Hz, 5-CH₂b), 3.87 (m, 1H,H-4′), 3.74 (dd, 1H, J=3.6 and 14.8 Hz, H-5′a), 3.66 (dd, 1H, J=3.6 and11.3 Hz, H-5′b), 2.41 (m, 1H, H-2′a), 2.03 (m, 1H, H-2′b), 0.90 (s, 9H,(CH₃)₃CSi), 0.87 (s, 9H, (CH₃)₃CSi), 0.83 (s, 9H, C(CH₃)₃), 0.09 (2 s,6H, (CH₃)₂Si), 0.06 (2 s, 6H, (CH₃)₂Si).

A solution of n-Bu₄NF (28 mg, 0.09 mmol) in THF (1.0 mL) was added to asolution of compound 46 (20 mg, 0.03 mmol) in THF (2.0 mL). The mixturewas stirred at room temperature for 30 min and concentrated in vacuo,and the residue was purified by silica gel column chromatography toyield5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine47 (11 mg, 82%). ¹H NMR (400 MHz, CD₃OD): δ 7.87 (s, 1H, H-6), 7.82 (dd,1H, J=1.2 and 8.4 Hz, Ph-H), 7.76 (dd, 1H, J=1.6 and 8.0 Hz, Ph-H), 7.68(m, 1H, Ph-H), 7.51 (m, 1H, Ph-H), 6.23 (t, 1H, J=6.6 Hz, H-1′), 4.94(s, 1H, Ph-CH), 4.44 (AB d, 1H, J=13.2 Hz, 5-CH₂a), 4.34 (m, 1H, H-3′),4.11 (AB d, 1H, J=13.2 Hz, 5-CH₂b), 3.88 (m, 1H, H-4′), 3.71 (dd, 1H,J=3.2 and 12.0 Hz, H-5′a), 3.63 (dd, 1H, J=4.0 and 12.0 Hz, H-5′b), 2.35(m, 1H, H-2′a), 2.14 (m, 1H, H-2′b), 0.80 (s, 9H, C(CH₃)₃).

Compound 47 (11 mg, 0.025 mmol) was phosphorylated with POCl₃ (7 μL,0.075 mmol) and proton sponge (11 mg, 0.05 mmol) in trimethylphosphate(0.3 mL) at 0° C. for three hours under a nitrogen atmosphere. Asolution of tri-n-butylammonium pyrophosphate (59 mg, 0.125 mmol) andtri-n-butylamine (30 μL) in anhydrous DMF (0.25 mL) was added. After 5min of stirring, triethylammonium bicarbonate buffer (1 M, pH 7.5; 5.0mL) was added. The reaction was stirred at room temperature for one hourand then lyophilized to dryness. The residue was dissolved in water (5.0mL), filtered, and purified by anion exchange chromatography. Thefractions containing triphosphate were combined and lyophilized to give5-[(S)-1-(2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine-5′-triphosphatedC.V, which was further purified using by RP-HPLC. HRMS (ESI): For themolecular ion C₂₁H₃₀N₄O₁₆P₃ [M−H]⁻, the calculated mass was 687.0870,and the observed mass was 687.0873.

5-[(S)-1-(5-Methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine-5′-triphosphate

To a solution of compound 39 (235 mg, 0.49 mmol) in anhydrous DMF (3.0mL), TBSCl (320 mg, 0.8 mmol) and imidazole (109 mg, 1.6 mmol) wereadded. The mixture was stirred at room temperature for six hours,concentrated in vacuo, dissolved in CH₂Cl₂ (20 mL), and washed withsaturated NaHCO₃ solution (50 mL). The organic and aqueous phases wereseparated, and the aqueous phase was extracted with CH₂Cl₂ (30 mL) threetimes. The combined organic phase was dried with Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel chromatography toyield3′,5′-O-bis-(tert-butyldimethylsilyl)-5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine48 (245 mg, 70%). ¹H NMR (400 MHz, CDCl₃): δ 8.00 (br s, 1H, NH), 7.88(d, J=9.2 Hz, 1H, Ph-H), 7.60 (s, 1H, H-6), 7.22 (d, 1H, J=2.8 Hz,Ph-H), 6.84 (dd, 1H, J=2.8 and 8.0 Hz, Ph-H), 6.25 (dd, 1H, J=5.6 and8.0 Hz, H-1′), 5.23 (s, 1H, Ph-CH), 4.40 (m, 1H, H-3′), 4.26 (d, 1H,J=12Hz, 5-CH₂a), 4.11 (d, 1H, J=12Hz, 5-CH₂b), 3.89 (m, 4H, OCH₃ andH-4′), 3.78 (m, 2H, H-5′), 2.27 (m, 1H, H-2′a), 2.04 (m, 1H, H-2′b),0.90 and 88 (2 s, 18H, SiC(CH₃)₃), 0.84 (s, 9H, C(CH₃)₃), 0.08 (3 s,12H, CH₃).

2,4,6-Triisopropyl benzenesulfonyl chloride (363 mg, 1.2 mmol) was addedto a solution of compound 48 (170 mg, 0.24 mmol), DMAP (32 mg, 0.26mmol), and triethylamine (0.34 mL, 2.4 mmol) in anhydrous CH₂Cl₂ (8.0mL). The mixture was stirred at room temperature overnight under anitrogen atmosphere, concentrated in vacuo, and the residue wasdissolved in a solution of NH₃ in 1,4-dioxane (0.5 M, 20 mL). Themixture was transferred into a sealed tube and was heated at 90° C.overnight. The mixture was cooled to room temperature, concentrated invacuo, dissolved in CH₂Cl₂ (20 mL), and washed with brine (50 mL). Theorganic and aqueous phases were separated, and the aqueous phase wasextracted with CH₂Cl₂ (30 mL) three times. The combined organic phasewas dried over Na₂SO₄, concentrated in vacuo, and the residue waspurified by silica gel column chromatography to yield3′,5′-O-bis-(tert-butyldimethylsilyl)-5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine49 (110 mg, 65% for two steps). ¹H NMR (400 MHz, DMSO-d₆): δ 7.96 (d,J=8.8 Hz, 1H, Ph-H), 7.50 (br s, 1H, NH₂), 7.38 (s, 1H, H-6), 7.08 (dd,1H, J=2.8 and 8.8 Hz, Ph-H), 7.04 (d, 1H, J=2.8 Hz, Ph-H), 6.80 (br s,1H, NH₂), 6.13 (t, 1H, J=6.4 Hz, H-1′), 5.09 (s, 1H, Ph-CH), 4.31 (m,1H, H-3′), 4.25 (d, 1H, J=12.8 Hz, 5-CH₂a), 4.08 (d, 1H, J=12.8 Hz,5-CH₂b), 3.87 (s, 3H, OCH₃), 3.76 (m, 1H, H-4′), 3.64 (m, 2H, H-5′),3.76 (dd, 1H, J=2.8 Hz, H-5′b), 2.10 (m, 1H, H-2′a), 2.00 (m, 1H,H-2′b), 0.87 (s, 9H, C(CH₃)₃), 0.78 and 0.76 (2 s, 18H, SiC(CH₃)₃),0.07, 0.06, −0.01, and −0.04 (4 s, 12H, SiCH₃).

To a solution of compound 49 (130 mg, 0.18 mmol) in THF (10 mL), n-Bu₄NF(141 mg, 0.44 mmol) was added. The mixture was stirred at roomtemperature for four hours, concentrated in vacuo, and the residue waspurified by silica gel column chromatography to yield5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine50 (72 mg, 82%). ¹H NMR (400 MHz, DMSO-d₆): δ 7.99 (d, J=8.0 Hz, 1H,Ph-H), 7.65 (s, 1H, H-6), 7.42 (br s, 1H, D₂O exchangeable, NH₂a), 7.06(m, 2H, Ph-H), 6.72 (br s, 1H, D₂O exchangeable, NH₂b), 6.11 (t, 1H,J=6.4 Hz, H-1′), 5.17 (d, 1H, D₂O exchangeable, 3′-OH), 5.12 (s, 1H,Ph-CH), 4.78 (t, 1H, D₂O exchangeable, 5′-OH), 4.25 (d, 1H, J=12.4 Hz,5-CH₂a), 4.15 (m, 1H, H-3′), 4.05 (d, 1H, J=12.4 Hz, 5-CH₂b), 3.87 (s,3H, OCH₃), 3.72 (m, 1H, H-4′), 3.44 (m, 2H, H-5′), 3.76 (dd, 1H, J=2.8Hz, H-5′b), 2.08 (m, 1H, H-2′a), 1.95 (m, 1H, H-2′b), 0.77 (s, 9H,C(CH₃)₃).

Compound 50 (20 mg, 0.043 mmol) was phosphorylated with POCl₃ (24 μL,0.26 mmol) and proton sponge (19 mg, 0.086 mmol) in trimethylphosphate(0.3 mL) at 0° C. for six hours under a nitrogen atmosphere. A solutionof tri-n-butylammonium pyrophosphate (237 mg, 0.50 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate buffer (0.1 M, pH 7.5; 10mL) was added. The reaction was stirred at room temperature for one hourand then concentrated in vacuo. The residue was dissolved in 20% aqueousacetonitrile (20 mL), filtered, and purified by anion exchangechromatography. The fractions containing triphosphate were combined andlyophilized to give5-[(S)-1-(5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine-5′-triphosphatedC.VI, which was further purified using RP-HPLC. HRMS (ESI): For themolecular ion C₂₂H₃₂N₄O₁₇P₃ [M−H]⁻, the calculated mass was 719.0975,and the observed mass was 719.0983.

Example 7 Synthesis of(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol and(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol

Nitric acid (68-70%, 125 mL) was slowly mixed with glacial acetic acid(125 ml) at room temperature, followed by addition of NaNO₂ (400 mg, 5.8mmol) and 3-iodoanisole (10 g, 42.7 mmol). After the reaction wasstirred at room temperature for 24 hours, I₂ (10.8 g, 42.7 mmol) wasadded and the mixture was stirred at 60° C. overnight. The reactionmixture was poured into ice-water (500 ml) and extracted by CH₂Cl₂ (100ml) three times. The combined organic phase was neutralized withsaturated NaHCO₃ solution (500 ml), washed with aqueous solution ofNa₂S₂O₃ (20%, 100 ml), dried over Na₂SO₄, and concentrated in vacuo. Theresidue was purified by silica gel column chromatography to yield crude3,6-diiodo-4-nitroanisole (5.4 g), which is mixed with one unknownby-product (20%) and used in the next step without further purification.¹H NMR (400 MHz, CDCl₃): δ 8.42 (s, 1H, Ph-H), 7.33 (s, 1H, Ph-H), 3.97(s, 3H, OCH₃).

To a solution of crude 3,6-diiodo-4-nitroanisole (770 mg, 80% purity,1.52 mmol) in anhydrous THF (10 mL) at minus 40° C. under a nitrogenatmosphere, phenylmagnesium chloride (2 M in THF, 0.46 mL, 0.92 mmol)was added dropwise at a rate such that the temperature would not exceedminus 35° C. Upon completion of the addition, the mixture was stirred atminus 40° C. for two hours, followed by addition oftrimethylacetaldehyde (0.22 mL, 1.97 mmol). The mixture was stirred atminus 30° C. for two hours and then at room temperature for another onehour. The reaction was then quenched with brine (1.0 mL), diluted withCH₂Cl₂ (100 mL), and the solution was washed with CH₃COOH (0.1 N, 50 ml)and brine (50 ml) sequentially. The organic phase was dried over Na₂SO₄,concentrated in vacuo, and the residue was purified by silica gel columnchromatography to yield racemic(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (399mg, 72%). ¹H NMR (400 MHz, CDCl₃): δ 8.32 (s, 1H, Ph-H), 7.17 (s, 1H,Ph-H), 5.60 (d, 1H, J=4.0 Hz, PhCH), 3.98 (s, 3H, OCH₃), 2.12 (d, 1H,J=4.0 Hz, OH), 0.89 (s, 9H, C(CH₃)₃).

To a solution of racemic(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (395mg, 1.1 mmol) and DMAP (263 mg, 2.16 mmol) in anhydrous CH₂Cl₂ (5.0 mL),(1S)-camphanic chloride (Corrie et al., 1992, which is incorporated byreference) (350 mg, 1.62 mmol) was added, and the mixture was stirredovernight at room temperature under a nitrogen atmosphere. The reactionmixture was diluted with CH₂Cl₂ (50 mL) and washed with saturated NaHCO₃solution (50 mL). The organic phase was dried over Na₂SO₄, concentratedin vacuo, and the residue was purified by silica gel columnchromatography to yield(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (490 mg, 80%, 1:1 mixture of diastereomers).

(R/S)-1-(4-Iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (3.4 g) was dissolved in boiling ethanol (150 ml), thesolution was kept in a warm oil bath and slowly cooled to roomtemperature and stood overnight. Needle crystals were formed graduallyand collected by filtration to yield pure single diastereomer(R)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (870 mg, 51%). The remaining mother liquor wasconcentrated in vacuo, and the residue was dissolved again in boilingethanol (150 ml), and the solution was quickly cooled to roomtemperature and needle crystals were formed within two hours. Thecrystals were collected by filtration to yield pure single diastereomer(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate. The crystallization process was repeated twice to yieldadditional pure (S)-diastereomer (total 1.07 g, 63%). ¹H NMR (400 MHz,CDCl₃) for (R)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate: δ 8.48 (s, 1H, Ph-H), 6.94 (s, 1H, Ph-H), 6.84 (s, 1H,Ph-CH), 3.93 (s, 3H, OCH₃), 2.42 (m, 1H, CH), 2.11 (m, 1H, CH), 1.92 (m,1H, CH₂), 1.75 (m, 1H, CH₂), 1.11 (s, 3H, CH₃), 1.05 (s, 3H, CH₃), 0.97(s, 9H, C(CH₃)₃), 0.86 (s, 3H, CH₃). ¹H NMR (400 MHz, CDCl₃) for(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate: 6 8.48 (s, 1H, Ph-H), 6.95 (s, 1H, Ph-H), 6.80 (s, 1H,Ph-CH), 3.96 (s, 3H, OCH₃), 2.37 (m, 1H, CH), 1.92 (m, 2H, CH₂), 1.66(m, 1H, CH), 1.14 (s, 3H, CH₃), 1.07 (s, 3H, CH₃), 1.06 (s, 3H, CH₃),0.98 (s, 9H, C(CH₃)₃).

A mixture of(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (1.1 g, 2.0 mmol) and K₂CO₃ (552 mg, 4.0 mmol) inmethanol (50 mL) was heated to reflux for one hour, then cooled down,concentrated in vacuo, and diluted with CH₂Cl₂ (50 mL). The organicphase was washed with brine (50 mL), dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel column chromatographyto yield enantiopure(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (720 mg,98%). ¹H NMR (400 MHz, CDCl₃): δ 8.32 (s, 1H, Ph-H), 7.17 (s, 1H, Ph-H),5.60 (d, 1H, J=4.0 Hz, PhCH), 3.98 (s, 3H, OCH₃), 2.12 (d, 1H, J=4.0 Hz,OH), 0.89 (s, 9H, C(CH₃)₃).

Example 8 Dye-labeled tBu-5-OMe-2-nitrobenzyl Alkylated HydroxymethylNucleotides Synthesis Synthesis of(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol and(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol

Nitric acid (68-70%, 125 mL) was slowly mixed with glacial acetic acid(125 ml) at room temperature, followed by addition of NaNO₂ (400 mg, 5.8mmol) and 3-iodoanisole (10 g, 42.7 mmol). After the reaction wasstirred at room temperature for 24 hours, I₂ (10.8 g, 42.7 mmol) wasadded and the mixture was stirred at 60° C. overnight. The reactionmixture was poured into ice-water (500 ml) and extracted by CH₂Cl₂ (100ml) three times. The combined organic phase was neutralized withsaturated NaHCO₃ solution (500 ml), washed with aqueous solution ofNa₂S₂O₃ (20%, 100 ml), dried over Na₂SO₄, and concentrated in vacuo. Theresidue was purified by silica gel column chromatography to yield crude3,6-diiodo-4-nitroanisole (5.4 g), which is mixed with one unknownby-product (20%) and used in the next step without further purification.¹H NMR (400 MHz, CDCl₃): δ 8.42 (s, 1H, Ph-H), 7.33 (s, 1H, Ph-H), 3.97(s, 3H, OCH₃).

To a solution of crude 3,6-diiodo-4-nitroanisole (770 mg, 80% purity,1.52 mmol) in anhydrous THF (10 mL) at minus 40° C. under a nitrogenatmosphere, phenylmagnesium chloride (2 M in THF, 0.46 mL, 0.92 mmol)was added dropwise at a rate such that the temperature would not exceedminus 35° C. Upon completion of the addition, the mixture was stirred atminus 40° C. for two hours, followed by addition oftrimethylacetaldehyde (0.22 mL, 1.97 mmol). The mixture was stirred atminus 30° C. for two hours and then at room temperature for another onehour. The reaction was then quenched with brine (1.0 mL), diluted withCH₂Cl₂ (100 mL), and the solution was washed with CH₃COOH (0.1 N, 50 ml)and brine (50 ml) sequentially. The organic phase was dried over Na₂SO₄,concentrated in vacuo, and the residue was purified by silica gel columnchromatography to yield racemic(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (399mg, 72%). ¹H NMR (400 MHz, CDCl₃): δ 8.32 (s, 1H, Ph-H), 7.17 (s, 1H,Ph-H), 5.60 (d, 1H, J=4.0 Hz, PhCH), 3.98 (s, 3H, OCH₃), 2.12 (d, 1H,J=4.0 Hz, OH), 0.89 (s, 9H, C(CH₃)₃).

To a solution of racemic(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (395mg, 1.1 mmol) and DMAP (263 mg, 2.16 mmol) in anhydrous CH₂Cl₂ (5.0 mL),(1S)-camphanic chloride (Corrie et al., 1992, which is incorporated byreference) (350 mg, 1.62 mmol) was added, and the mixture was stirredovernight at room temperature under a nitrogen atmosphere. The reactionmixture was diluted with CH₂Cl₂ (50 mL) and washed with saturated NaHCO₃solution (50 mL). The organic phase was dried over Na₂SO₄, concentratedin vacuo, and the residue was purified by silica gel columnchromatography to yield(R/S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (490 mg, 80%, 1:1 mixture of diastereomers).

(R/S)-1-(4-Iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (3.4 g) was dissolved in boiling ethanol (150 ml), thesolution was kept in a warm oil bath and slowly cooled to roomtemperature and stood overnight. Needle crystals were formed graduallyand collected by filtration to yield pure single diastereomer(R)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (870 mg, 51%). The remaining mother liquor wasconcentrated in vacuo, and the residue was dissolved again in boilingethanol (150 ml), and the solution was quickly cooled to roomtemperature and needle crystals were formed within two hours. Thecrystals were collected by filtration to yield pure single diastereomer(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate. The crystallization process was repeated twice to yieldadditional pure (S)-diastereomer (total 1.07 g, 63%). ¹H NMR (400 MHz,CDCl₃) for (R)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate: 6 8.48 (s, 1H, Ph-H), 6.94 (s, 1H, Ph-H), 6.84 (s, 1H,Ph-CH), 3.93 (s, 3H, OCH₃), 2.42 (m, 1H, CH), 2.11 (m, 1H, CH), 1.92 (m,1H, CH₂), 1.75 (m, 1H, CH₂), 1.11 (s, 3H, CH₃), 1.05 (s, 3H, CH₃), 0.97(s, 9H, C(CH₃)₃), 0.86 (s, 3H, CH₃). ¹H NMR (400 MHz, CDCl₃) for(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1propyl(1S)-camphanate: 6 8.48 (s, 1H, Ph-H), 6.95 (s, 1H, Ph-H), 6.80(s, 1H, Ph-CH), 3.96 (s, 3H, OCH₃), 2.37 (m, 1H, CH), 1.92 (m, 2H, CH₂),1.66 (m, 1H, CH), 1.14 (s, 3H, CH₃), 1.07 (s, 3H, CH₃), 1.06 (s, 3H,CH₃), 0.98 (s, 9H, C(CH₃)₃).

A mixture of(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propyl(1S)-camphanate (1.1 g, 2.0 mmol) and K₂CO₃ (552 mg, 4.0 mmol) inmethanol (50 mL) was heated to reflux for one hour, then cooled down,concentrated in vacuo, and diluted with CH₂Cl₂ (50 mL). The organicphase was washed with brine (50 mL), dried over Na₂SO₄, concentrated invacuo, and the residue was purified by silica gel column chromatographyto yield enantiopure(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (720 mg,98%). ¹H NMR (400 MHz, CDCl₃): δ 8.32 (s, 1H, Ph-H), 7.17 (s, 1H, Ph-H),5.60 (d, 1H, J=4.0 Hz, PhCH), 3.98 (s, 3H, OCH₃), 2.12 (d, 1H, J=4.0 Hz,OH), 0.89 (s, 9H, C(CH₃)₃).

Synthesis of dye labeled7-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyadenosine-5′-triphosphateand 5′-α-thiotriphosphate

DMAP (463 mg, 3.80 mmol) and MsCl (177 μL, 2.28 mmol) were added to asolution of compound 4 (400 mg, 0.76 mmol) in anhydrous CH₂Cl₂ (5.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 mins and at room temperature for another 3 hours. The reactionwas then diluted with CH₂Cl₂ (20 mL). The solution was applied on ashort silica gel plug (2×3 cm) and was eluted quickly with ahexane/ethyl acetate/triethylamine solvent system (80 mL, volume ratio:80/20/0.5). The eluent was concentrated in vacuo, and the residue wasmixed with(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (500 mg,1.37 mmol). The mixture was heated at 115° C. for 45 min under anitrogen atmosphere, cooled to room temperature and dissolved in THF (10mL). n-Bu₄NF (526 mg, 1.67 mmol) was added and the mixture was stirredat room temperature for 12 hours and then concentrated in vacuo. Theresidue was dissolved in CH₂Cl₂ (50 mL) and washed with brine (50 mL),and the aqueous phase was extracted with CH₂Cl₂ (20 mL) two times. Thecombined organic phase was dried over Na₂SO₄, concentrated in vacuo, andthe residue was purified by silica gel chromatography to yield6-chloro-9-(β-D-2′-deoxyribofuranosyl)-7-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]-methyl-7-deazapurine51 (135 mg, 29% for three steps). ¹H NMR (400 MHz, CDCl₃): δ 8.56 (s,1H, H-2), 8.21 (s, 1H, Ph-H), 7.34 (s, 1H, H-8), 7.02 (s, 1H, Ph-H),6.35 (dd, 1H, J=6.0 and 8.8 Hz, H-1′), 5.20 (s, 1H, Ph-CH), 4.76 (dd,2H, J=12.4 and 36.4 Hz, 7-CH₂), 4.74 (m, 1H, H-3′), 4.13 (m, 1H, H-4′),3.96 (m, 1H, H-5′a), 3.92 (s, 3H, OCH₃), 3.80 (m, 1H, H-5′b), 2.85 (m,1H, H-2′a), 2.30 (m, 1H, H-2′b), 0.83 (s, 9H, C(CH₃)₃).

Compound 51 (135 mg, 0.22 mmol) was dissolved in 1,4-dioxane (10 mL)followed by addition of NH₃ in MeOH (7 N, 20 mL). The mixture wastransferred to a sealed tube and stirred at 100° C. for 24 hours, thencooled to room temperature, concentrated in vacuo, and the residue waspurified by silica gel chromatography to yield7-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyadenosine52 (110 mg, 80%). ¹H NMR (400 MHz, CDCl₃): δ 8.24 (s, 1H, H-2), 8.22 (s,1H, Ph-H), 6.96 (s, 1H, Ph-H), 6.79 (s, 1H, H-8), 6.14 (dd, 1H, J=6.0and 7.6 Hz, H-1′), 5.21 (s, 1H, Ph-CH), 4.74 (m, 1H, H-3′), 4.56 (dd,2H, J=13.2 and 24.8 Hz, 7-CH₂), 4.17 (m, 1H, H-4′), 3.93 (m, 1H, H-5′a),3.83 (s, 3H, OCH₃), 3.79 (m, 1H, H-5′b), 2.96 (m, 1H, H-2′a), 2.21 (m,1H, H-2′b), 0.83 (s, 9H, C(CH₃)₃).

A solution of compound 52 (183 mg, 0.29 mmol),N-propargyltrifluoroacetylamide (435 mg, 2.9 mmol),tetrakis(triphenylphosphine)-palladium(0) (66 mg, 0.057 mmol), CuI (21mg, 0.11 mmol), and Et₃N (170 μL, 1.22 mmol) in anhydrous DMF (4.0 mL)was stirred at 50° C. for 24 hours. The mixture was concentrated invacuo and purified by silica gel column chromatography to yield7-{(S)-1-[5-methoxy-4-(3-trifluoroacetamido-1-propynyl)-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyadenosine53 (185 mg, 98%). ¹H NMR (400 MHz, MeOH-d₄): δ 8.06 (s, 1H, H-2), 7.89(s, 1H, Ph-H), 7.17 (s, 1H, H-8), 7.15 (s, 1H, Ph-H), 6.37 (dd, 1H,J=6.0 and 7.6 Hz, H-1′), 5.23 (s, 1H, Ph-CH), 4.68 (d, 1H, J=12.8 Hz,7-CH₂a), 4.49 (m, 1H, H-3′), 4.34 (s, 2H, CH₂), 3.97 (m, 1H, H-4′), 3.86(s, 3H, OCH₃), 3.70 (m, 2H, H-5′), 2.59 (m, 1H, H-2′a), 2.2.8 (m, 1H,H-2′b), 0.85 (s, 9H, C(CH₃)₃).

Compound 53 (52 mg, 0.08 mmol) was phosphorylated with POCl₃ (14 μL,0.15 mmol) and proton sponge (34 mg, 0.16 mmol) in trimethylphosphate(0.5 mL) at 0° C. for 3 hours under a nitrogen atmosphere. A solution ofbis-tri-n-butylammonium pyrophosphate (237 mg, 0.5 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate solution (TEAB, 0.1 M, pH7.5; 10 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing triphosphate were combined andlyophilized to dryness. The residue was dissolved in water (10 mL) andtreated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield7-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyadenosine-5′-triphosphate54a, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₇H₃₆N₆O₁₆P₃ [M−H]⁻,the calculated mass was 793.1401, and the observed mass was 793.1426.

Compound 53 (91 mg, 0.14 mmol) was thiophosphorylated with PSCl₃ (14 μL,0.14 mmol) and 2,4,6-collidine (34 mg, 0.28 mmol) in triethylphosphate(1.0 mL) at 0° C. for 1 hour under a nitrogen atmosphere. A solution ofbis-tri-n-butylammonium pyrophosphate (332 mg, 0.7 mmol) andtri-n-butylamine (140 μL) in anhydrous DMF (1.4 mL) was added. After 2min of stirring, triethylammonium bicarbonate solution (TEAB, 1 M, pH7.5; 20 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing thiotriphosphate were combinedand lyophilized to dryness. The residue was dissolved in water (10 mL)and treated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield7-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyadenosine-5′-α-thiotriphosphate54b, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₇H₃₆N₆O₁₅P₃S[M−H]⁻, the calculated mass was 809.1172, and the observed mass was809.1155.

A solution of Alexa Fluor 488 NHS (5 mg, 7.8 μmol) in anhydrous DMSO(200 μL) was added to a solution of triphosphate Ma (1.6 μmol) inNaHCO₃/Na₂CO₃ buffer (0.1 M, pH 9.2, 0.4 mL). The mixture was left atroom temperature in dark for one hour. The mixture was first purified byanion exchange HPLC on a Dionex DNApac PA200 column (250×4 mm). Mobilephase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing dye labeled triphosphate 55a werecombined and concentrated to small volume, and the product was furtherpurified by reverse phase HPLC on a PerkinElmer Aquapore OD-300 column(7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

A solution of Alexa Fluor 488 NHS (5 mg, 7.8 μmol) in anhydrous DMSO(200 μL) was added to a solution of thiotriphosphate 54b (4.1 μmol) inNaHCO₃/Na₂CO₃ buffer (0.1 M, pH 9.2, 1.0 mL). The mixture was left atroom temperature in dark for one hour. The mixture was first purified byanion exchange chromatography using a Q Sepharose FF column (2.5×10 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing dye labeled thiotriphosphate 55bwere combined and lyophilized to dryness, and the product was furtherpurified by reverse phase HPLC on a PerkinElmer Aquapore OD-300 column(7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

Synthesis of dye labeled7-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyguanosine-5′-triphosphateand 5′-α-thiotriphosphate

DMAP (502 mg, 4.1 mmol) and MsCl (238 μL, 3.1 mmol) were added to asolution of compound 18 (680 mg, 1.0 mmol) in anhydrous CH₂Cl₂ (6.0 mL)at 0° C. under a nitrogen atmosphere. The reaction was stirred at 0° C.for 10 min and then diluted with CH₂Cl₂ (20 mL). The solution wasapplied on a short silica gel plug (2×3 cm) and was eluted quickly witha hexane/ethyl acetate/triethylamine solvent system (80 mL, volumeratio: 80/20/0.5). The eluent was concentrated in vacuo, and the residuewas mixed with(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (500 mg,2.1 mmol). The mixture was heated at 115° C. for 45 min under a nitrogenatmosphere, cooled to room temperature and dissolved in THF (10 mL).n-Bu₄NF (1.07 g, 3.40 mmol) was added and the mixture was stirred atroom temperature for 12 hours and then concentrated in vacuo. Theresidue was dissolved in CH₂Cl₂ (50 mL) and washed with brine (50 mL),and the aqueous phase was extracted with CH₂Cl₂ (20 mL) two times. Thecombined organic phase was dried over Na₂SO₄, concentrated in vacuo, andthe residue was purified by silica gel chromatography to yield2-amino-6-chloro-9-(β-D-2′-deoxyribofuranosyl)-7-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]-methyl-7-deazapurine56 (125 mg, 18% for three steps). ¹H NMR (400 MHz, CDCl₃): δ 8.24 (s,1H, Ph-H), 7.04 (s, 1H, Ph-H), 6.91 (s, 1H, H-8), 6.17 (dd, 1H, J=6.0and 8.4 Hz, H-1′), 5.18 (s, 1H, Ph-CH), 5.11 (br s, 2H, NH₂), 4.71 (m,1H, H-3′), 4.59 (dd, 2H, J=12.4 and 24.4 Hz, 7-CH2), 4.13 (m, 1H, H-4′),3.96 (s, 3H, OCH₃), 3.88 (m, 1H, H-5′a), 3.79 (m, 1H, H-5′b), 2.76 (m,1H, H-2′a), 2.32 (m, 1H, H-2′b), 0.81 (s, 9H, (CH₃)₃).

To a solution of compound 56 (100 mg, 0.16 mmol) in 1,4-dioxane (1.5 mL)and DMF (3.0 mL), syn-pyrimidine-2-aldoxime (389 mg, 3.2 mmol) and1,1,3,3-tetramethyl guanidine (439 μL, 3.5 mmol) were added, and themixture was heated at 70° C. overnight under a nitrogen atmosphere. Thereaction mixture was diluted with CH₂Cl₂ (20 mL) and washed sequentiallywith acetic acid solution (0.1 M, 50 mL), saturated NaHCO₃ solution (50mL), and brine (50 mL). The organic phase was dried over Na₂SO₄,concentrated in vacuo, and the residue was purified by silica gelchromatography to yield7-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-7-deaza-2′-deoxyguanosine57 (70 mg, 72%). ¹H NMR (400 MHz, MeOH-d₄): δ 8.20 (s, 1H, Ph-H), 7.17(s, 1H, Ph-H), 6.82 (s, 1H, H-8), 6.18 (m, 1H, H-1′), 5.23 (s, 1H,Ph-CH), 4.71 (d, 1H, J=12.0 Hz, 7-CH₂a), 4.52 (d, 1H, J=12.0 Hz,7-CH₂b), 4.43 (m, 1H, H-3′), 3.97 (s, 3H, OCH₃), 3.91 (m, 1H, H-4′),3.71 (m, 2H, H-5′), 2.49 (m, 1H, H-2′a), 2.19 (m, 1H, H-2′b), 0.85 (s,9H, (CH₃)₃).

A solution of compound 57 (50 mg, 0.08 mmol),N-propargyltrifluoroacetylamide (117 mg, 0.8 mmol),tetrakis(triphenylphosphine)-palladium(0) (18 mg, 0.02 mmol), CuI (5.9mg, 0.03 mmol), and Et₃N (48 μL, 0.34 mmol) in anhydrous DMF (3.0 mL)was stirred at 50° C. for 12 hours. The mixture was concentrated invacuo and the residue was purified by silica gel column chromatographyto yield7-{(S)-1-[5-methoxy-4-(3-trifluoroacetamido-1-propynyl)-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyguanosine58 (50 mg, 96%). ¹H NMR (400 MHz, MeOH-d₄): δ 7.87 (s, 1H, Ph-H), 7.26(s, 1H, Ph-H), 6.84 (s, 1H, H-8), 6.20 (m, 1H, H-1′), 5.25 (s, 1H,Ph-CH), 4.67 (d, 1H, J=12.0 Hz, 7-CH₂a), 4.54 (d, 1H, J=12.0 Hz,7-CH₂b), 4.43 (m, 1H, H-3′), 4.33 (s, 2H, CH₂), 3.95 (s, 3H, OCH₃), 3.89(m, 1H, H-4′), 3.70 (m, 2H, H-5′), 2.46 (m, 1H, H-2′a), 2.18 (m, 1H,H-2′b), 0.86 (s, 9H, (CH₃)₃).

Compound 58 (52 mg, 0.08 mmol) was phosphorylated with POCl₃ (27 μL, 0.3mmol) and proton sponge (33 mg, 0.16 mmol) in trimethylphosphate (0.35mL) at 0° C. for 4 hours under a nitrogen atmosphere. A solution ofbis-tri-n-butylammonium pyrophosphate (237 mg, 0.5 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate solution (TEAB, 0.1 M, pH7.5; 10 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing triphosphate were combined andlyophilized to dryness. The residue was dissolved in water (10 mL) andtreated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield7-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyguanosine-5′-triphosphate59a, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₇H₃₆N₆O₁₇P₃ [M−H]⁻,the calculated mass was 809.1350, and the observed mass was 809.1360.

Compound 59 (50 mg, 0.075 mmol) was thiophosphorylated with PSCl₃ (9 μL,0.09 mmol) and 2,4,6-collidine (18 mg, 0.15 mmol) in triethylphosphate(0.5 mL) at room temperature for 2.5 hours under a nitrogen atmosphere.A solution of bis-tri-n-butylammonium pyrophosphate (237 mg, 0.5 mmol)and tri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After2 min of stirring, triethylammonium bicarbonate solution (TEAB, 1 M, pH7.5; 20 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing thiotriphosphate were combinedand lyophilized to dryness. The residue was dissolved in water (10 mL)and treated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield7-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-7-deaza-2′-deoxyguanosine-5′-α-thiotriphosphate59b, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₇H₃₆N₆O₁₆P₃S[M−H]⁻, the calculated mass was 825.1121, and the observed mass was825.1103.

A solution of Alexa Fluor 594 NHS (4.2 mg, 5.2 μmol) in anhydrous DMSO(170 μL) was added to a solution of triphosphate 59a (2.2 μmol) inNaHCO₃/Na₂CO₃ buffer (0.1 M, pH 9.2, 0.5 mL). The mixture was left atroom temperature in dark for one hour. The mixture was first purified byanion exchange HPLC on a Dionex DNApac PA200 column (250×4 mm). Mobilephase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing dye labeled triphosphate 60a werecombined and concentrated to small volume, and the product was furtherpurified by reverse phase HPLC on a PerkinElmer Aquapore OD-300 column(7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

A solution of Alexa Fluor 594 NHS (5 mg, 6.2 μmol) in anhydrous DMSO(200 μL) was added to a solution of thiotriphosphate 59b (4.45 μmol) inNaHCO₃/Na₂CO₃ buffer (0.1 M, pH 9.2, 0.78 mL). The mixture was left atroom temperature in dark for one hour. The mixture was first purified byanion exchange chromatography using a Q Sepharose FF column (2.5×10 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing dye labeled thiotriphosphate 60bwere combined and concentrated to small volume, and the product wasfurther purified by reverse phase HPLC on a PerkinElmer Aquapore OD-300column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

Synthesis of dye labeled5-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxyuridine-5′-triphosphateand 5′-α-thiotriphosphate

Compound 38 (350 mg, 0.54 mmol) and(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-1-propanol (720 mg,1.97 mmol) were heated at 110° C. for 45 min under a nitrogenatmosphere. The mixture was cooled down to room temperature, dissolvedin MeOH (10 mL), and followed by addition of NH₄F (400 mg, 11.1 mmol).The mixture was stirred at 50° C. for 12 hours, concentrated in vacuo,dissolved in CH₂Cl₂ (50 mL), and washed with brine (50 mL). The organicphase was dried over Na₂SO₄, concentrated in vacuo, and the residue waspurified by silica gel chromatography to yield5-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine61 (90 mg, 28%). ¹H NMR (400 MHz, CDCl₃): δ 8.34 (s, 1H, Ph-H), 7.65 (s,1H, H-6), 7.12 (s, 1H, Ph-H), 6.17 (t, 1H, J=6.8 Hz, H-1′), 5.18 (s, 1H,Ph-CH), 4.59 (m, 1H, H-3′), 4.27 (d, 1H, J=12.0 Hz, 5-CH₂a), 4.15 (d,1H, J=12.0 Hz, 5-CH₂b), 4.00 (m, 1H, H-4′), 3.97 (s, 3H, OCH₃), 3.95 (m,1H, H-5′a), 3.82 (m, 1H, H-5′b), 2.34 (m, 2H, H-2), 0.84 (s, 9H,C(CH₃)₃).

A solution of compound 61 (80 mg, 0.13 mmol),N-propargyltrifluoroacetylamide (196 mg, 1.30 mmol),tetrakis(triphenylphosphine)-palladium(0) (30 mg, 0.026 mmol), CuI (9.9mg, 0.052 mmol), and Et₃N (80 μL) in anhydrous DMF (3.0 mL) was stirredat 50° C. for 12 hours. The mixture was concentrated in vacuo and theresidue was purified by silica gel column chromatography to yield5-{(S)-1-[5-methoxy-4-(3-trifluoroacetamido-1-propynyl)-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxyuridine62 (75 mg, 90%). ¹H NMR (400 MHz, MeOD-d₄): δ 8.11 (s, 1H, H-6), 8.08(s, 1H, Ph-H), 7.36 (s, 1H, Ph-H), 6.27 (t, 1H, J=6.4 Hz, H-1′), 5.33(s, 1H, Ph-CH), 4.47 (m, 1H, H-3′), 4.44 (s, 2H, 5-CH₂), 4.32 (d, 2H,J=2.0 Hz, CH2), 4.08 (s, 3H, OCH₃), 3.99 (m, 1H, H-4′), 3.87 (m, 1H,H-5′a), 3.79 (m, 1H, H-5′b), 2.30 (m, 2H, H-2), 0.93 (s, 9H, C(CH₃)₃).

Compound 62 (40 mg, 0.064 mmol) was phosphorylated with POCl₃ (21 μL,0.22 mmol) and proton sponge (27 mg, 0.13 mmol) in trimethylphosphate(0.35 mL) at 0° C. for 4 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.5 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate solution (TEAB, 0.1 M, pH7.5; 10 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing triphosphate were combined andlyophilized to dryness. The residue was dissolved in water (10 mL) andtreated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield5-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxyuridine-5′-triphosphate63a, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile.

Compound 62 (130 mg, 0.21 mmol) was thiophosphorylated with PSCl₃ (26μL, 0.25 mmol) and 2,6-lutidine (89 mg, 0.84 mmol) in triethylphosphate(0.6 mL) at room temperature for 1 hour under a nitrogen atmosphere. Asolution of bis-tri-n-butylammonium pyrophosphate (474 mg, 1.0 mmol) andtri-n-butylamine (200 μL) in anhydrous DMF (2.0 mL) was added. After 2min of stirring, triethylammonium bicarbonate solution (TEAB, 1 M, pH7.5; 20 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing thiotriphosphate were combinedand lyophilized to dryness. The residue was dissolved in water (10 mL)and treated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield5-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxyuridine-5′-α-thiotriphosphate63b, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₅H₃₄N₄O₁₇P₃S[M−H]⁻, the calculated mass was 787.0853, and the observed mass was787.0884.

A solution of Alexa Fluor 532 NHS (2 mg, 2.76 μmol) in anhydrous DMSO(80 μL) was added to a solution of triphosphate 62a (1.07 μmol) inNaHCO₃/Na₂CO₃ buffer (0.1 M, pH 9.2, 0.3 mL). The mixture was left atroom temperature in dark for one hour. The mixture was first purified byanion exchange HPLC on a Dionex DNApac PA200 column (250×4 mm). Mobilephase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing dye labeled triphosphate 63a werecombined and concentrated to small volume, and the product was furtherpurified by reverse phase HPLC on a PerkinElmer Aquapore OD-300 column(7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

A solution of Alexa Fluor 532 NHS (2.5 mg, 3.45 μmol) in anhydrous DMSO(100 μL) was added to a solution of thiotriphosphate 62b (1.03 μmol) inNaHCO₃/Na₂CO₃ buffer (0.1 M, pH 9.2, 0.15 mL). The mixture was left atroom temperature in dark for one hour. The mixture was first purified byanion exchange chromatography using a Q Sepharose FF column (2.5×10 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing dye labeled thiotriphosphate 63bwere combined and lyophilized to dryness, and the product was furtherpurified by reverse phase HPLC on a PerkinElmer Aquapore OD-300 column(7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

Synthesis of dye labeled5-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxycytidine-5′-triphosphateand 5′-α-thiotriphosphate

To a solution of compound 61 (295 mg, 0.49 mmol) in anhydrous DMF (5.0mL), TBSCl (185 mg, 1.23 mmol) and imidazole (160 mg, 2.35 mmol) wereadded. The mixture was stirred at room temperature for 12 hours,concentrated in vacuo, and dissolved in CH₂Cl₂ (50 mL). The solution waswashed with saturated NaHCO₃ solution (50 mL) and the aqueous phase wasextracted with CH₂Cl₂ (30 mL) three times. The combined organic phasewas dried with Na₂SO₄, concentrated in vacuo, and the residue waspurified by silica gel chromatography to yield3′,5′-O-bis-(tert-butyldimethylsilyl)-5-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxyuridine65 (400 mg, 96%). ¹H NMR (400 MHz, CDCl₃): δ 8.32 (s, 1H, Ph-H), 7.64(s, 1H, H-6), 7.12 (s, 1H, Ph-H), 6.12 (t, 1H, J=6.8 Hz, H-1′), 5.20 (s,1H, Ph-CH), 4.60 (m, 1H, H-3′), 4.25 (d, 1H, J=12.0 Hz, 5-CH₂a), 4.14(d, 1H, J=12.0 Hz, 5-CH₂b), 4.02 (m, 1H, H-4′), 3.97 (s, 3H, OCH₃), 3.94(m, 1H, H-5′a), 3.83 (m, 1H, H-5′b), 2.34 (m, 2H, H-2), 0.90 and 88 (2s, 18H, SiC(CH₃)₃), 0.84 (s, 9H, C(CH₃)₃), 0.08 (3 s, 12H, CH₃).

2,4,6-Triisopropyl benzenesulfonyl chloride (581 mg, 1.92 mmol) wasadded to a solution of compound 65 (400 mg, 0.48 mmol), DMAP (64 mg,0.53 mmol), and triethylamine (0.60 mL, 4.32 mmol) in anhydrous CH₂Cl₂(15 mL). The mixture was stirred at room temperature overnight under anitrogen atmosphere, concentrated in vacuo, and the residue wasdissolved in a solution of NH₃ in 1,4-dioxane (0.5 M, 20 mL). Themixture was transferred into a sealed tube and was heated at 90° C.overnight. The reaction was then cooled to room temperature,concentrated in vacuo, and the residue was dissolved in THF (8.0 mL)followed by addition of n-Bu₄NF (333 mg, 1.06 mmol). The mixture wasstirred at room temperature for four hours, concentrated in vacuo, andthe residue was purified by silica gel column chromatography to yield5-[(S)-1-(4-iodo-5-methoxy-2-nitrophenyl)-2,2-dimethyl-propyloxy]methyl-2′-deoxycytidine66 (240 mg, 83% for three steps in total). ¹H NMR (400 MHz, MeOD-d₄): δ8.33 (s, 1H, Ph-H), 7.91 (s, 1H, H-6), 7.10 (s, 1H, Ph-H), 6.16 (t, 1H,J=6.4 Hz, H-1′), 5.19 (s, 1H, Ph-CH), 4.41 (d, 1H, J=12.4 Hz, 5-CH₂a),4.33 (m, 1H, H-3′), 4.26 (d, 1H, J=12.4 Hz, 5-CH₂b), 3.97 (s, 3H, OCH₃),3.88 (m, 1H, H-4′), 3.70 (m, 2H, H-5′), 2.34 (m, 1H, H-2′a), 2.17 (m,1H, H-2′b), 0.84 (s, 9H, C(CH₃)₃).

A solution of compound 66 (245 mg, 0.4 mmol),N-propargyltrifluoroacetylamide (603 mg, 4.0 mmol),tetrakis(triphenylphosphine)-palladium(0) (92 mg, 0.8 mmol), CuI (30 mg,0.16 mmol), and Et₃N (240 μL, 1.7 mmol) in anhydrous DMF (5.0 mL) wasstirred at 50° C. for 12 hours. The mixture was concentrated in vacuoand purified by silica gel column chromatography to yield5-{(S)-1-[5-methoxy-4-(3-trifluoroacetamido-1-propynyl)-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxycytidine67 (230 mg, 91%). ¹H NMR (400 MHz, MeOD-d₄): δ 7.98 (s, 1H, Ph-H), 7.92(s, 1H, H-6), 7.19 (s, 1H, Ph-H), 6.15 (t, 1H, J=6.4 Hz, H-1′), 5.21 (s,1H, Ph-CH), 4.41 (d, 1H, J=13.2 Hz, 5-CH₂a), 4.33 (m, 3H, H-3′ and CH₂),4.27 (d, 1H, J=13.2 Hz, 5-CH₂b), 3.96 (s, 3H, OCH₃), 3.88 (m, 1H, H-4′),3.72 (m, 2H, H-5′), 2.30 (m, 1H, H-2′a), 2.12 (m, 1H, H-2′b), 0.84 (s,9H, C(CH₃)₃).

Compound 67 (45 mg, 0.072 mmol) was phosphorylated with POCl₃ (15 μL,0.16 mmol) and proton sponge (31 mg, 0.14 mmol) in trimethylphosphate(0.35 mL) at 0° C. for 4 hours under a nitrogen atmosphere. A solutionof bis-tri-n-butylammonium pyrophosphate (237 mg, 0.5 mmol) andtri-n-butylamine (100 μL) in anhydrous DMF (1.0 mL) was added. After 10min of stirring, triethylammonium bicarbonate solution (TEAB, 0.1 M, pH7.5; 10 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing triphosphate were combined andlyophilized to dryness. The residue was dissolved in water (10 mL) andtreated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield5-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxycytidine-5′-triphosphate68a, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₅H₃₅N₅O₁₇P₃ [M−H]⁻,the calculated mass was 770.1241, and the observed mass was 770.1234.

Compound 67 (118 mg, 0.19 mmol) was thiophosphorylated with PSCl₃ (24μL, 0.23 mmol) and 2,6-lutidine (80 mg, 0.75 mmol) in triethylphosphate(0.5 mL) at 0° C. for 1 hour under a nitrogen atmosphere. A solution ofbis-tri-n-butylammonium pyrophosphate (474 mg, 1.0 mmol) andtri-n-butylamine (200 μL) in anhydrous DMF (2.0 mL) was added. After 2min of stirring, triethylammonium bicarbonate solution (TEAB, 1 M, pH7.5; 20 mL) was added. The reaction was stirred at room temperature forone hour and then concentrated in vacuo. The residue was dissolved in75% 0.1 M TEAB/25% acetonitrile (20 mL), filtered, and purified by anionexchange chromatography using a Q Sepharose FF column (2.5×20 cm).Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 M TEAB/25%acetonitrile. The fractions containing thiotriphosphate were combinedand lyophilized to dryness. The residue was dissolved in water (10 mL)and treated with concentrated ammonium hydroxide (10 mL, 27%) at roomtemperature for one hour to yield5-{(S)-1-[4-(3-amino-1-propynyl)-5-methoxy-2-nitrophenyl]-2,2-dimethyl-propyloxy}methyl-2′-deoxycytidine-5′-α-thiotriphosphate68b, which was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile. HRMS (ESI): For the molecular ion C₂₅H₃₅N₅O₁₆P₃S[M−H]⁻, the calculated mass was 786.1012, and the observed mass was786.0983.

A solution of Cy5 NHS (5 mg, 6.3 μmol) in anhydrous DMSO (200 μL) wasadded to a solution of triphosphate 68a (1.59 μmol) in NaHCO₃/Na₂CO₃buffer (0.1 M, pH 9.2, 0.35 mL). The mixture was left at roomtemperature in dark for one hour. The dye labeled triphosphate was firstpurified by anion exchange HPLC on a Dionex DNApac PA200 column (250×4mm). Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B, 75% 1.5 MTEAB/25% acetonitrile. The fractions containing dye labeled triphosphate69a were combined and concentrated to small volume, and the product wasfurther purified by reverse phase HPLC on a PerkinElmer Aquapore OD-300column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB; B, acetonitrile.

A solution of Cy5 NHS (5 mg, 6.3 μmol) in anhydrous DMSO (200 μL) wasadded to a solution of thiotriphosphate 68b (2.96 μmol) in NaHCO₃/Na₂CO₃buffer (0.1 M, pH 9.2, 0.53 mL). The mixture was left at roomtemperature in dark for one hour. The dye labeled thiotriphosphate wasfirst purified by anion exchange chromatography using a Q Sepharose FFcolumn (2.5×10 cm). Mobile phase: A, 75% 0.1 M TEAB/25% acetonitrile; B,75% 1.5 M TEAB/25% acetonitrile. The fractions containing dye labeledthiotriphosphate 69b were combined and lyophilized to dryness, and theproduct was further purified by reverse phase HPLC on a PerkinElmerAquapore OD-300 column (7 μm, 250×4.6 mm). Mobile phase: A, 0.1 M TEAB;B, acetonitrile.

All of the methods disclosed and claimed herein can be made and executedwithout undue experimentation in light of the present disclosure. Whilethe compositions and methods of this invention have been described interms of certain embodiments, it will be apparent to those of skill inthe art that variations may be applied to the methods and in the stepsor in the sequence of steps of the method described herein withoutdeparting from the concept, spirit and scope of the invention. Morespecifically, it will be apparent that certain agents which are bothchemically and physiologically related may be substituted for the agentsdescribed herein while the same or similar results would be achieved.All such similar substitutes and modifications apparent to those skilledin the art are deemed to be within the spirit, scope and concept of theinvention as defined by the appended claims.

Example 9 UV Photocleavage Studies

The rate of UV photocleavage was found to be dependent on a number ofexperimental factors including light intensity. See McCray et al. (1980)and McGall et al. (1997), which are both incorporated herein byreference. To compare the rates of photochemical cleavage between thenucleotide analogs described here, a protocol was developed to deliver adaily light intensity output of 0.70±0.01 W/cm² to samples, see below. Acustom-designed UV deprotector used in these studies has been previouslydescribed in Wu et al. (2007), which is incorporated herein byreference, and the protocol implemented is described below.

UV Deprotector Set-Up:

The power supply was turned on for about 30 min prior to that of thelamp and recirculation bath as described by the manufacturer. The IRliquid filter was cooled to 9° C. Light intensity was determined using amodel PM100 power meter (Thorlabs), a 1000 μm pinhole (Edmund Optics), amodified 0.5 mL Eppendorf tube cut in half, and a 3-axis manualtranslation stage (Newport), see FIG. 5. The half cut Eppendorf tube waspositioned in front of the pinhole and power meter detector head toaccount for the geometric shape distortion of the light as it passesthrough a reaction solution. The translation stage was then used toalign the tube/pinhole/detector device with the highest intensity fromthe arc beam.

Intensity adjustment to 0.7 W/cm²: To stabilize its output, the lamp wasleft on for one hour prior to intensity measurements. Thereafter, themeasured power was adjusted by increasing the current from the powersupply. In order to achieve intensity (I) of 0.70 W/cm², the measuredpower (P) was adjusted to ˜5.5 mW, according to the equation:

$I = \frac{P}{\pi \times r^{2}}$

where r is the radius of pinhole. Power readings are recorded over afive minute period (in one second intervals) and were converted intointensity readings, which ranged over a six week period between0.68±0.01 and 0.72±0.02 W/cm².

Beam Alignment with the 0.5 mL Tube Holder:

The modified Eppendorf tube, pin hole and power meter were then removedfrom the UV deprotector, and the rotating sample holder was installedwith the height being 67.18±0.25 mm. The beam was then focused byplacing an 0.5 mL Eppendorf tube into the sample holder, the tube ofwhich was modified with an internal alignment card to provide referencelines for volume heights of 10 μL and 20 μL, see FIG. 5. The referencelines enabled the beam to be centered for a given reaction volume. Beamalignment was further verified by observing the mercury arc image of thelamp produced by the rear reflector. A second alignment card was placedinto the rotating sample holder to view the image, which when properlyaligned using the reflector would produce an inverted arc image on thearc gap itself. This step ensured that arc hotspots were notsuperimposed, which could cause overheating while maintaining a poweroutput of ˜5.5 mW. The speed of the rotating sample holder was adjustedwithin a range of 1,200-1,350 rpm using a Nova-Strobe DA Plusstroboscope (Monarch Instrument) by adjusting the motor's torque with anadjustment screw.

Photochemical Cleavage Assays:

Nucleotide analogs were incorporated using 10 μL reactions, as describedfor the PEP assays, at a final concentration of 100 nM. See Litosh etal. (2011), which is incorporated herein by reference. OligoTemplate-2,oligoTemplate-5, and oligoTemplate-4 each hybridized with BODIPY-FLlabeled primer-1 were used for C⁷-HOMedA, C⁷-HOMedG, and HOMedU analogs,respectively. OligoTemplate-8 hybridized with BODIPY-FL labeled primer-3was used to assay HOMedC analogs. Incorporated reactions were quenchedwith either 1 mM sodium azide solution; 1 mM sodium azide, 50 mM DTTsolution; or reagents C-G (see key in FIG. 4), exposed to 365 nmultraviolet (UV) light for various time points using our UV deprotector,and then placed on ice. Ten μL of stop solution (98% deionizedformamide; 10 mM Na₂EDTA, pH 8.0; 25 mg/mL Blue Dextran, MW 2,000,000)was added, and samples were analyzed using an AB model 377 DNAsequencer. Cleavage assays were performed in triplicate to calculate theaverage DT₅₀ value±1 SD, as described in Litosh et al. (2011), which isincorporated herein by reference.

REFERENCES

The following references, and those listed in the Appendix, to theextent that they provide exemplary procedural or other detailssupplementary to those set forth herein, are specifically incorporatedherein by reference.

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1-56. (canceled)
 57. A method of identifying a plurality of bases in atarget nucleic acid comprising the following steps: (i) attaching the5′-end of a primer to a solid surface; (ii) hybridizing a target nucleicacid to the primer attached to the solid surface to form a hybridizedprimer/target nucleic acid complex; (iii) obtaining a polymerase and acompound of formulas I-VII, with the proviso that compounds of differentformulas I-VII have different reporters:

wherein: R₁ is triphosphate or α-thiotriphosphate; R₂ is hydrogen orhydroxy; R₃ is alkyl_((C≦8)) or substituted alkyl_((C≦8)); R₄ ishydrogen, hydroxy, halo, amino, nitro, cyano, azido or mercapto;alkyl_((C≦6)), acyl_((C≦6)), alkoxy_((C≦6)), acyloxy_((C≦6)),alkylamino_((C≦6)), dialkylamino_((C≦6)), amido_((C≦6)), or asubstituted version of any of these groups; R₅ is a -linker-reporter,wherein the reporter is based on a dye; R₆ is: hydrogen, hydroxy, halo,amino, nitro, cyano, azido or mercapto; alkyl_((C≦6)), alkenyl_((C≦6)),alkynyl_((C≦6)), aryl_((C≦6)), aralkyl_((C≦8)), heteroaryl_((C≦6)),acyl_((C≦6)), alkoxy_((C≦6)), acyloxy_((C≦6)), alkylamino_((C≦6)),dialkylamino_((C≦6)), amido_((C≦6)), or a substituted version of any ofthese groups; or a salt, tautomer, or optical isomer thereof; (iv)reacting the hybridized primer/target nucleic acid complex with apolymerase and one or more of the compounds of step (iii) to form agrowing primer strand via a polymerase reaction; (v) imaging the growingprimer strand to identify the incorporated compound of step (iv) via itsreporter; (vi) exposing the solid surface with the growing primer strandto a light source to remove a photocleavable terminating moiety of theformula:

with the variables as defined by the claim referenced in step (iii); and(vii) repeating steps (iv) through (vi) one or more times to identify aplurality of bases in the target nucleic acid, where the extended primerof step (vi) of the previous cycle reacts in place of the hybridizedprimer/target nucleic acid complex in step (iv) of the subsequent cycle.58-60. (canceled)
 61. The method of claim 57, wherein step (vi) isconducted in the presence of sodium acetate. 62-63. (canceled)
 64. Themethod of claim 57, wherein steps (v) or (vi) is conducted in thepresence of thiourea. 65-66. (canceled)
 67. The method of claim 57,wherein step (vi) is conducted in the presence of dithiothreitol (DTT).68. A method of identifying a plurality of bases in a target nucleicacid comprising the following steps: (i) attaching the 5′-end of atarget nucleic acid to a solid surface; (ii) hybridizing a primer to thenucleic acid attached to the solid surface to form a hybridizedprimer/target nucleic acid complex; (iii) obtaining a polymerase and acompound of formulas I-VII, with the proviso that compounds of differentformulas I-VII have different reporters:

wherein: R₁ is triphosphate or α-thiotriphosphate; R₂ is hydrogen orhydroxy; R₃ is alkyl_((C≦8)) or substituted alkyl_((C≦8)); R₄ ishydrogen, hydroxy, halo, amino, nitro, cyano, azido or mercapto;alkyl_((C≦6)), acyl_((C≦6)), alkoxy_((C≦6)), acyloxy_((C≦6)),alkylamino_((C≦6)), dialkylamino_((C≦6)) amido_((C≦6)), or a substitutedversion of any of these groups; R₅ is a -linker-reporter, wherein thereporter is based on a dye; R₆ is: hydrogen, hydroxy, halo, amino,nitro, cyano, azido or mercapto; alkyl_((C≦6)), alkenyl_((C≦6)),alkynyl_((C≦6)), aryl_((C≦6)), aralkyl_((C≦8)), heteroaryl_((C≦6)),acyl_((C≦6)), alkoxy_((C≦6)), acyloxy_((C≦6)), alkylamino_((C≦6)),dialkylamino_((C≦6)), amido_((C≦6)), or a substituted version of any ofthese groups; or a salt, tautomer, or optical isomer thereof; or a salt,tautomer, or optical isomer thereof; (iv) reacting the hybridizedprimer/target nucleic acid complex with a polymerase and one or more ofthe compounds of step (iii) to form a growing primer strand via apolymerase reaction; (v) imaging the growing primer strand to identifythe incorporated compound of step (iv) via its reporter; (vi) exposingthe solid surface with the growing primer strand to a light source toremove a photocleavable terminating moiety of the formula:

with the variables as defined by the claim referenced in step (iii); and(vii) repeating steps (iv) through (vi) one or more times to identify aplurality of bases in the target nucleic acid, where the extended primerof step (vi) of the previous cycle reacts in place of the hybridizedprimer/target nucleic acid complex in step (iv) of the subsequent cycle.69. (canceled)
 70. The method of claim 68, wherein step (vi) isconducted in the presence of dithiothreitol (DTT).
 71. The method ofclaim 57, wherein the incorporation of at least one compound accordingto step (iv) occurs at about 70% to about 100% of the efficiency ofincorporation of its natural nucleotide counterpart.
 72. The method ofclaim 71, wherein the incorporation efficiency occurs at about 85% toabout 100%.
 73. The method of claim 57, wherein the polymerase isselected from the group consisting of reverse transcriptase, terminaltransferase, and DNA polymerase.
 74. The method of claim 57, whereinabout 85% to about 100% of the photocleavable terminating moieties areremoved by exposure to a light source in step (vi).
 75. The method ofclaim 57, wherein incorporation of at least one compound according tostep (iv) is followed by termination of strand growth at an efficiencyof from about 90% to about 100%. 76-78. (canceled)
 79. The method ofclaim 57, further comprising prior to step (iv) capping any primers orgrowing primer strands that did not react in step (iv).
 80. The methodof claim 57, further comprising sequencing multiple target nucleic acidssynchronistically. 81-115. (canceled)
 116. The compound of claim 57,wherein R₁ is a triphosphate.
 117. The compound of claim 57, wherein R₁is an α-thiotriphosphate.
 118. The compound of claim 57, wherein R₃ isalkyl_((C≦8)).
 119. The compound of claim 118, wherein R₃ isalkyl_((C3-4)).
 120. The compound of claim 119, wherein R₃ istert-butyl.
 121. The compound of claim 57, wherein R₄ is hydrogen. 122.The compound of claim 57, wherein the linker of the -linker-reporter is:

wherein X is —O—, —S—, or —NH—; or alkanediyl_((C≦12)),alkenediyl_((C≦12)), alkynediyl_((C≦12)), arenediyl_((C≦12)),heteroarenediyl_((C≦12)), or a substituted version of any of thesegroups; and n is an integer from 0-6.
 123. The compound of claim 122,wherein X is —C≡C—.
 124. The compound of claim 122, wherein n is zero.125. The compound of claim 57, wherein the dye is a zanthene,fluorescein, rhodamine, BODIPY, cyanine, coumarin, pyrene,phthalocyanine, phycobiliprotein, or a squaraine dye.
 126. The compoundof claim 57, wherein the reporter is:


127. The compound of claim 57, wherein R₆ is hydrogen.
 128. The compoundof claim 57, wherein the starred carbon atom is in the S configuration.